Also known as
Model type Modular
Model part of larger framework
Note on status model
Date note status model
Incorporated models or components:
Spatial dimensions 3D
Spatial extent Global, Patch-Scale
Model domain Marine, Carbonates and Biogenics
One-line model description Population-ecology based model of shallow-ocean benthic carbonate accumulation
Extended model description The carbonate production is modelled according to organism growth and survival rates moderated by habitat suitability (chiefly light, temperature, nutrient). The environmental inputs are extracted from global databases. At the seabed the model's vertical zonation allows for underground (diagenetic) processes, bed granular transport, lower stable framework, upper collapsable framework. This voxelation allows for the carbonate to be placed (accumulated) correctly within the bedding and clast fabrics. The stratigraphy and seabed elevation are built in this way. As conditions change (e.g., by shallowing) the biological communities respond in the simulation, and so too do the production rates and clast/binding arrangements. Events punctuate the record, and the organism assemblages adjust according to frequencies and severities. The population stocks are calculated by diffuse competition in a Lotke-Volterra scheme, or via cellular simulations of close-in interactions to represent competition by growth, recruitment.

carbonate sediments, population ecology, numerical model, benthic colonial organisms,

Name Chris Jenkins
Type of contact Project manager
Institute / Organization INSTAAR Univ Colorado at Boulder
Postal address 1 1560 30th St
Postal address 2 UCB 450
Town / City Boulder
Postal code 80309-0450
State Colorado
Country United States
Email address
Phone +1 720 840 3303
Fax +1 303-492-6388

Supported platforms
Other platform
Programming language


Other program language
Code optimized Single Processor
Multiple processors implemented
Nr of distributed processors
Nr of shared processors
Start year development 2010
Does model development still take place? Yes
If above answer is no, provide end year model development
Code development status
When did you indicate the 'code development status'?
Model availability
Source code availability
(Or provide future intension)
Source web address
Source csdms web address
Program license type Other
Program license type other --
Memory requirements Usual PC
Typical run time 2 hours for 1000 year run

Describe input parameters Model setup: grid extent and resolution, time stepping and duration.

Environmental inputs (from global datasets, automated methods): bathymetry, seawater bottom temperatures, benthic irradiance, seafloor hardness, ocean wave climate Organism characteristics (automated from Knowledge Base): dimensions, construction, reproduction and survivorship

Input format ASCII, Binary
Other input format
Describe output parameters Benthic carbonate accumulation; sediment character and thickness; organism stocks and remains; environmental history; 2D-3D map graphics; graphs of stocks and vacant seafloor through time.
Output format ASCII
Other output format
Pre-processing software needed? No
Describe pre-processing software
Post-processing software needed? No
Describe post-processing software
Visualization software needed? No
If above answer is yes
Other visualization software

Describe processes represented by the model Population ecology represented by diffuse competition Lotke-Volterra calculus, cellular automaton, cellular stochastic models.

Sediment transport arbitrated by slopes and wave energy pickup Bioerosion scaled to the seafloor presence of skeletal material

Describe key physical parameters and equations Bathymetry, seawater temperatures, ocean wave climate, benthic irradiance, seafloor hardness
Describe length scale and resolution constraints Cells are approximately 1-1000m in scale; map areas 10-100km on side.
Describe time scale and resolution constraints Timestepping is usually annual, extending over 1000 years. However the model is capable of doing finer and longer runs.
Describe any numerical limitations and issues Usual Python limitations on floating point precision. ODE's are solved on scales much finer than annual, and their performance is monitored.

Describe available calibration data sets The model produces virtual core-logs which can be compared with Ocean Drilling Program and other descriptive core logs and with outcrops.
Upload calibration data sets if available:
Describe available test data sets
Upload test data sets if available:
Describe ideal data for testing

Do you have current or future plans for collaborating with other researchers? Yes
Is there a manual available? Yes
Upload manual if available:
Model website if any
Model forum / discussion board
Comments Email to for further details, manual, code, collaboration

This part will be filled out by CSDMS staff

OpenMI compliant No but possible
BMI compliant No but possible
WMT component No but possible
PyMT component
Is this a data component
Can be coupled with:
Model info
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Total citations: 0
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m-quotient: 0

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Input Files

Output Files