DEMENTpy — MMRT Version

DEcomposition Model of ENzymatic Traits in Python, modified to calculate temperature-dependent reaction rates using Macromolecular Rate Theory (MMRT).

A spatially explicit, trait-based model of microbial decomposition. The model simulates a grid of microbial taxa competing for substrates via extracellular enzymes, tracking carbon and energy flow through degradation, uptake, metabolism, mortality, and reproduction over repeated climate pulses.

Author: Jeth Walkup, PhD — Department of Ecology and Evolutionary Biology, University of California Irvine (jethwalkup@gmail.com / jwalkup@uci.edu)

Repository layout

src/        Core model code (DEMENTpy engine)
  dementpy.py        Main driver / simulation loop
  initialization.py  Builds the initial ecosystem from input CSVs
  grid.py            Spatial grid; degradation, uptake, metabolism, etc.
  microbe.py         Microbial taxa and traits
  enzyme.py          Extracellular enzyme pool
  substrate.py       Substrate pool
  monomer.py         Monomer pool
  output.py          Output collection and export (CSV / NetCDF / Zarr)
  utility.py         Helper functions

input/      Model inputs (parameters, runtime config, climate data)
  runtime.txt        Simulation settings (grid size, taxa, pulses, etc.)
  parameters.csv     Model parameters
  climate.csv        Climate forcing
  ...                Additional trait / substrate / enzyme input tables

analysis/   Post-processing and figure-generation scripts
submit_multi_climate.sh   SLURM array job for HPC (UCI HPC3 / Green Planet)

Requirements

Python 3 with the packages in requirements.txt:

pip install -r requirements.txt

Core dependencies: numpy, pandas, scipy, xarray, matplotlib. Optional output backends: netCDF4 (NetCDF output) and zarr (Zarr output).

Running the model

The driver reads command-line arguments and expects to be run from inside src/:

cd src
python dementpy.py <input_folder> <output_folder> <output_name> [climate_file]

• input_folder — name of the input directory (e.g. input)
• output_folder — name of the directory to write results to
• output_name — label for this run (digits in the name seed the RNG)
• climate_file — optional climate CSV (default: climate.csv)

Example:

cd src
python dementpy.py input output run001 climate.csv

Configuration

Simulation settings live in input/runtime.txt, including grid dimensions (x, y), number of taxa and enzymes, number of pulses and time steps (end_time), output interval, and output_format (csv, netcdf, or zarr).

HPC / batch runs

submit_multi_climate.sh is a SLURM array script for running many communities across multiple climate scenarios on a cluster. Run bash submit_multi_climate.sh --help-style inspection of the header for options (community directory, climate source, partition, etc.).

License

No license has been added yet. Without a license, default copyright applies and others have no legal right to use, modify, or distribute this code. A license can be added later.