LSSE-Mega is a reaction-transport model for simulating sediment geochemistry.
In 2013 it got a new graphical user interface, thanks to the UROP project of Josh Erspamer.
Download: LSSE-Mega :
Geochemical model description:
The model's structure and the numerical Fortran code for this version are described in Katsev
et al. 2007 and its Appendix.
If you use the results from this model in publications, please refer to this paper. Other publications that used LSSE-Mega are listed below.
Running the model
The interface (LSSE.jar) will run on any
platform, though the model code (file diag_main.exe) will run only on
a PC (sorry, no suitable compilers for Mac). Download the model and
unzip it in its own directory. You should be able to run it by clicking
on LSSE.jar. You may need to install Java on your computer.
A very brief tutorial
The graphical interface is intended to facilitate interation with the
model code and should make it easier for an uninitiated user to delve
into diagenetic modeling. The numerical heart of the model is the
Fortran code that is compilied into the 'diag_main.exe' file. It communicates with the interface via two files:
the vertical profiles of the simulated chemical species. It also serves
to specify the initial condition from which the model is run. The model
overwrites this file regularly during the run and also places the final
results there. The graphical interface reads out the results from this
file and displays them as concentrations-vs-depth graphs, which are
updated during program execution.
the model parameters. It is read by the code at the beginning of the
run. The graphical interface makes it easier to navigate through these
parameters, which are written into the Constants.txt file before the
An advanced user may want to have a greater control over the model. For this purpose, I include the folder 'FortranUser'.
It contains the original Fortran code and the command-line compilers
that are necessary to compile it into the new diag_main.exe file. The
file 'UserFunctions.f' contains the functions that a typical user would be most likely to modify: the depth dependences of the sediment porosity and the bioturbation and bioirrigation
intensities. To make modifications to these functions, follow these
steps: a) Make needed corrections to the functions and save
UserFunctions.f; b) Run 'compile.bat'. This should generate a new diag_main.exe file in the FortranUser directory. c) Copy this file into the 'data' directory, overwriting the old file.
In the provided version of the code, the model starts from the initial
condition defined in Data.txt and runs for the specified period of
time, which is defined by the parameter TFINAL (in the
Parameters/Simulation tabs.). In most typical applications of the
model, a user would want to choose this time sufficiently large so that
the model achieves the steady state. Though the model does simulate the
time evolution of the system, the provided code is intended primarily
for steady state investigations, as certain time-dependent features
have not been yet implemented in the graphical interface (though they
do exist within the Fortran code).
Hints: a) To avoid
numerical difficulties, start your simulations simple and build
complexity gradually. For example, start by checking only the
checkboxes for organic matter and oxygen. This will limit the number of
chemical reactions considered. Run the model to steady state. Then add
more species, one by one. b) Bioturbation generally improves numerical
convergence, whereas bioirrigation may cause difficulties. Start by
having buiturbation and no bioirrigation, and adjust them gradually. c)
Convergence generally improves for higher sediment burial rates, as the
chemical gradients are less sharp in that case. d) Copy your successful
Data.txt and Constants.txt files into separate files using the
respective 'Save as' buttons. Should you run into numerical
difficulties later, you will be able to restart by reading your initial
conditions from these files.
What does the model's name mean?
LSSE originally stood for 'Lake Sediment Structure and Evolution',
which was the name of the research group at the University of Ottawa
where I wrote the initial version of the code. The 'Mega' part is a
testament to youthful megalomania.
Li, J., & Katsev, S. (2014). Nitrogen cycling in deeply oxygenated
sediments: Results in Lake Superior and implications for marine
sediments. Limnology and Oceanography, 59(2), 465-481. (PDF)
Katsev, S. & M. Dittrich (2013) Modeling of decadal-scale
phosphorus retention in lake sediments under varying redox conditions.
Ecological Modeling 251: 246-259 (PDF).
Katsev, S. (2007) Modeling of sediment-water exchanges over multi-year
time scales. Proceedings of the workshop “Perspectives of Lake
Modeling: Towards Predicting Reaction to Trophic Change. Berlin,
November 8-9, 2007.
Katsev, S., G. Chaillou, B. Sundby, and A. Mucci (2007) Effect of
progressive oxygen depletion on sediment diagenesis and fluxes: A model
for the Lower St. Lawrence Estuary. Limnology and Oceanography 52:
Katsev, S., I. Tsandev, I. L’Heureux, and D.G. Rancourt (2006) Factors
controlling long term phosphorus efflux in lake sediments: Exploratory
reaction-transport modeling, Chemical Geology 234, 127-147. (PDF)
Katsev, S., B. Sundby, and A. Mucci (2006) Modeling vertical migrations
of the redox boundary in sediments: Application to deep basins of the
Arctic Ocean. Limnology and Oceanography 51, 1581-1593. (PDF)