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Mystic

An inferred biomass biogeochemical model of Mystic Lake.

Dependencies

  • Matlab (developed with version 8)
  • Python (developed with version 2.7)

Installation

$ git clone http://github.com/almlab/mystic.git

File structure

  • analysis/: Tool for plotting timecourses and the profiles for rates and concs.
  • bin/: Main matlab scripts.
  • simulation/: Scripts for running the model with easily-adjustable parameters and displaying the output.
  • lake.cfg: Configuration for the simulation.
  • README.md: This file.

Usage

Interactive

To run the model,

  • Update lake.cfg with the desired parameters.
  • Under simulation, use write_default_values_script.py to create run_interactive_defaults.m, which supplies the values in lake.cfg to interactive.m.
  • In Matlab, run run_interactive.m. This requires the bin/ folder to be on Matlab's path. If running in the terminal, you can use the set_matlab_path.py script to do this.
  • The output of the simulation is stored in concs_history and rates_history variables. You can write them to files using bin/write_data_to_files.m.

Analysis

To make timecourses and end-time plots for all the rates and chemical concentrations, copy the desired history.mat data file to analysis/ and run analysis/profiles/pipeline.sh.