PyBMFT-C

Bay-Marsh-Forest Transect with Carbon model

About

This is a Python version of the Coastal Landscape Transect model (CoLT) from Valentine et al. (2023). CoLT is originally written in Matlab, and expands upon the Bay Marsh Forest Transect model (BMFT) from Kirwan et al. (2016) by integrating carbon cycling dynamics. See Valentine et al. (2023) for a full description of the model.

This Python version of CoLT - PyBMFT-C - is used in the BarrierBMFT coupled model framework (Reeves et al., in review) and differs from the original Matlab version of CoLT with the following ALTERATIONS/NEW ADDITIONS:

1. PyBMFT-C does not contain the option to disperse autochthonous carbon with depth, and therefore only deposits autochthonous carbon on the surface of the marsh
2. Sediment supply to the marsh platform is allowed past the first drowned/ponded cell (evolvemarsh.py)
3. The organic content of bay sediment is held constant at 5% (bmftc.py)
4. Marsh edge progradation and bay accretion are recorded to depositional record, and marsh progradation is included in flux of sediment from bay to marsh; eroded sediment is removed from the depositional record (bmftc.py)
5. The density of the marsh edge cell is calculated using the most recent year where the elevation of the marsh is above the depth of erosion, rather than the first year (bmftc.py)

Installation

To download the source code for PyBMFT-C, either clone the repository with git:

git clone [email protected]/UNC-CECL/pybmft-c

or download the zip file:

https://github.com/UNC-CECL/PyBMFT-C/archive/refs/heads/main.zip

Then, run the following from the top-level folder (the one that contains setup.py) to install PyBMFT-C into the current environment:

pip install -e .

Input Files & Parameters

Input files for running a standalone PyBMFT-C simulation (i.e., not within BarrierBMFT) are located in the PyBMFT-C/Input directory. See documentation in the CoLT repository for additional information on input files. PyBMFT-C parameter values can be set in the initialization of the PyBMFT-C classes within a run script (see example below).

Example Simulation

The following describes the approach for running a standalone PyBMFT-C simulation. For a more comprehensive example run script, see run_bmftc.py.

To run PyBMFT-C, first set the working direcory to the main PyBMFT-C directory.

Then, import PyBMFT-C and dependencies:

from bmftc import Bmftc  
import numpy as np
import matplotlib.pyplot as plt

Next, initialize an instance of the PyBMFT-C class. Here, you can set certain parameter values such as the simulation duration (time step count; yrs), RSLR rate (mm/yr), or the external suspended sediment supply (reference concentration; mg/L). Parameters values not set here will revert to their default values:

bmftc = Bmftc(
            name="PyBMFT-C Example Simulation",
            time_step_count=50,
            relative_sea_level_rise=4,
            reference_concentration=50,
)
print(bmftc.name)

Next, run the simulation by progressing through time:

for time_step in range(int(bmftc.dur)):

    # Print time step to screen
    print("\r", "Time Step: ", time_step, end="")

    # Run time step
    bmftc.update()

Once the simulation finishes, we can plot some results. For example, the following plots the elevation profile for every 10^th year:

plt.figure()
for t in range(bmftc.startyear, bmftc.endyear, 10):
    plt.plot(bmftc.elevation[t, :])
plt.xlabel("Distance")
plt.ylabel("Elevation [m MSL]")
plt.title(bmftc.name)

References

CoLT (Coastal Landscape Transect model)

Code: https://github.com/csdms-contrib/colt
Wiki: https://csdms.colorado.edu/wiki/Model:Coastal_Landscape_Transect_Model_(CoLT)
DOI: 10.5281/zenodo.7625873

Valentine, K., Herbert, E. R., Walters, D. C., Chen, Y., Smith, A. J., & Kirwan, M. L. (2023). Climate-driven tradeoffs 
between landscape connectivity and the maintenance of the coastal carbon sink. Nature Communications, 14, 1137. 
https://doi.org/10.1038/s41467-023-36803-7.

BMFT (Bay-Marsh-Forest Transect model)

Kirwan, M. L., Walters, D. C., Reay, W. G., & Carr, J. A. (2016). Sea level driven marsh expansion in a coupled model 
of marsh erosion and migration. Geophysical Research Letters, 43, 4366–4373. https://doi.org/10.1002/2016GL068507

BarrierBMFT (Barrier Bay-Marsh-Forest Transect model)

Code: https://github.com/UNC-CECL/BarrierBMFT
Wiki: TBD
DOI: TBD

Reeves, I.R.B., Moore, L.J., Valentine, K., Fagherazzi, S., & Kirwan, M.L. (in review). Sediment exchange across coastal 
barrier landscapes alters ecosystem extents.