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https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem
A process based Dynamic Vegetation, Dynamic Organic Soil, Terrestrial Ecosystem Model.
https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem
carbon-cycling ecosystem-modeling fire-dynamics permafrost-dynamics soil-thermal-dynamics vegetation-dynamics
Last synced: about 2 months ago
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A process based Dynamic Vegetation, Dynamic Organic Soil, Terrestrial Ecosystem Model.
- Host: GitHub
- URL: https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem
- Owner: uaf-arctic-eco-modeling
- License: mit
- Created: 2012-06-07T01:26:42.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2024-06-14T19:04:07.000Z (7 months ago)
- Last Synced: 2024-06-17T14:37:27.674Z (7 months ago)
- Topics: carbon-cycling, ecosystem-modeling, fire-dynamics, permafrost-dynamics, soil-thermal-dynamics, vegetation-dynamics
- Language: Jupyter Notebook
- Homepage:
- Size: 114 MB
- Stars: 20
- Watchers: 15
- Forks: 23
- Open Issues: 133
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - dvm-dos-tem - A process based Dynamic Vegetation, Dynamic Organic Soil, Terrestrial Ecosystem Model. (Biosphere / Plants and Vegetation)
README
README for dvm-dos-tem
===========================================
[](https://zenodo.org/badge/latestdoi/4579979)
[](https://arctic-eco-modeling.slack.com)
The dvm-dos-tem (`dvmdostem`) model is a process based bio-geo-chemical
ecosystem model that focuses on C and N dynamics as well as soil thermal
dynamics in high latitude ecosystems.
For more information see the [User Guide](https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/index.html).
For questions and to get involved please see the [Github Issues](https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/issues) and [Github Discussions](https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/discussions).
> [!NOTE]
> **Whats with the name?** `dvm-dos-tem` is short for "**D**ynamic
> **V**egetation \[**M**odel\] **D**ynamic **O**rganic **S**oil **T**errestrial
> **E**cosystem **M**odel". Orignally the model was simply "TEM", and as more
> logic and capabilities have been added, the name has grown. We still
> frequently use simply "TEM" because it is less cumbersome for writing and
> typing. In most context TEM, dvmdostem, dvm-dos-tem, DVM-DOS-TEM and DMVDOSTEM
> are synonomous and can be used interchangably.
## Quickstart
For users who have Docker and Git installed.
More details are available in the [User Guide - Basic Model Setup and Run](https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/examples_and_tutorials/basic_model_run.html#basic-model-setup-and-run).
The default settings will run the model in the source code directory, using the
sample data that is included with the repository in the ``demo-data/`` directory.
The run will output a single variable (GPP), and will run for 2 pixels.
- Clone the repository (``git clone https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem.git``).
- Change into directory (``cd dvm-dos-tem``).
- Get some input data (optional).
- Make Docker usable by non-root user (optional).
- Build Docker images (``./docker-build-wrapper.sh cpp-dev && ./docker-build-wrapper.sh dev``).
- Setup your environment variables in ``.env`` file for ``V_TAG``, ``DDT_INPUT_CATALOG``, and ``DDT_WORKFLOWS`` (optional).
- Start Docker containers (``V_TAG=$(git describe) docker compose up -d dvmdostem-dev``).
- Obtain shell in container (``docker compose exec dvmdostem-dev bash``)
- Compile code (``develop@56ef79004e31:/work$ make``)
- Setup working directory (optional).
- Change into working directory (optional) .
- Adjust as needed (optional):
- Your run mask (``run-mask.nc``)
- The outputs you would like to generate (``output_spec.csv``)
- Any other configuration items (``config.js``)
- Any custom parameters (``parameters/``)
- Any custom target data (``calibration/calibration_targets.py``).
- Start the model run (``develop@56ef79004e31:/work$ ./dvmdostem --log-level monitor -p 100 -e 1000 -s 250 -t 115 -n 85``).
- Analyze run (``develop@56ef79004e31:/work$ ./scripts/plot_output_var.py --yx 0 0 --file output/GPP_yearly_tr.nc``).
> [!WARNING]
> Sept 2022 - We are in the process of updating the entire documentation
> system. There is still info scattered across this README, the wiki, a Google
> Doc and the Sphinx system but we are working on consolidating the info into
> primarily the Sphinx system (the User Guide).