licensing and wip readmes

README.md

@@ -6,32 +6,51 @@ SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
 
 # DO+BGC (Dissolved Oxygen and BioGeoChemistry)
 
-**DO+BGC** is a family of models for Dissolved Oxygen Dynamics plus simple biogeochemistry implemented in `FABM`.
+**DO+BGC** is a family of models for Dissolved Oxygen Dynamics plus simple BioGeoChemistry implemented in `FABM`.
 
 ## Description
-**DO+BGC** includes:
+Currently **DO+BGC** includes:
 
 * `OxyPOM` (**Oxygen + Particulate Organic Matter**): Simulates oxygen consumption and production in river based on [Holzwarth and Wirtz, 2018](https://doi.org/10.1016/j.ecss.2018.01.020). 
 * `DiaMo` (**Diagnostic Model**): Simulates oxygen consumption and production using a statistical inspired model (WIP). 
 
-The code of these models is located in the directory `.\src\oxypom` and `.\src\diamo`, and future code developed as part of this model should be here included.
+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.
 
-## Installation and usage
-* Requires the last version of `FABM` and the last version of `GOTM`.
-* The model is run with the script `gotm-installation.sh`   
+## Requirements
+
+* This model requires:
+    - `FABM` (v1 or above) available in [fabm github](https://github.com/fabm-model/fabm/)    
+
+The following is not required to build and run the model but it is for running the test case:
+
+* The physical driver:
+    - `GOTM` (tested with v6) available in [gotm github](https://github.com/orgs/gotm-model/repositories)
+
+* 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
-Currently, we include a testcases using `GOTM` as physical driver in the Elbe `estuary` in 2005-2024.
-To run the testcase go to the directory `.\testcases`.
 
-* The last version of `GOTM` and `FABM` is required as well as a FORTRAN compiler and CMake.
+We provide the model with a testcase in the directory `.\testcases`.
+New testcases for **DO+BGC** should be included in a single directory within `.\testcases`.
+Currently, we include the testcase estuary.
 
-* These variables must be defined: 
+### Testcase Estuary
+This setup uses the physical driver `GOTM` to simulate the water column dynamics in the Elbe estuary in 2005-2024.
+
+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: 
     - `GOTMDIR` base directory of GOTM source code
     - `FABMDIR` base directory of FABM source code
     - `DOBGCPDIR` base directory of dobgcp source code
 
-In this testcase they are defined as:
+By default they are:
 
 ```
 export GOTMDIR=$HOME/tools/gotm/code
@@ -39,8 +58,7 @@ export FABMDIR=$HOME/tools/fabm/fabm
 export DOBGCPDIR=$HOME/tools/dobgcp/src
 ```
 
-* The model is build with the script `gotm-installation.sh`. 
-This script creates the directory `.\build` with the building files, and a copy of `gotm` executable in the `.\estuary` directory.
+* 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`.
 
@@ -52,11 +70,13 @@ The downloaded files are used under license [DL-DE->Zero-2.0](https://www.govdat
 * Run the model with `./gotm`. It generates the files `output.nc` and `restart.nc`.
 
 * 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 total procedure is:
+Summarizing, the entire procedure is:
 
 ```
 bash gotm-installation.sh
@@ -67,8 +87,6 @@ Rscript setup_data.R
 RScript plot_output.R
 ```
 
-New testcases for this model need to be here included.
-
 ## To do
 - [ ] Create the complete script for the testcases
 - [ ] surface oxygen in DiaMo is not working well.
@@ -77,7 +95,7 @@ New testcases for this model need to be here included.
 - [ ] check the right licensing for this code
 
 ## License
-CC0-1.0
+Apache-2.0
 
 ## Project status
 This is part of the `DAM-ElbeXtreme` project.
\ No newline at end of file

src/diamo/README.md

-!! SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
-!! SPDX-License-Identifier: CC0-1.0
-!! SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
\ No newline at end of file
+<!---
+SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
+SPDX-License-Identifier: CC0-1.0
+SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
+-->
\ No newline at end of file

src/diamo/diamo.F90

 !! SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
-!! SPDX-License-Identifier: CC0-1.0
+!! SPDX-License-Identifier: Apache-2.0
 !! SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
 
 #include "fabm_driver.h"

src/oxypom/README.md

-!! SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
+<!---
+SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
 !! SPDX-License-Identifier: CC0-1.0
-!! SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
\ No newline at end of file
+!! SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
+-->
\ No newline at end of file

src/oxypom/oxypom.F90

 !! SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
-!! SPDX-License-Identifier: CC0-1.0
+!! SPDX-License-Identifier: Apache-2.0
 !! SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
 
 !! FABM implementation for biogeochemical model described in: