The deep time paleo modeler is responsible for creating the ocean bathymetry, the ocean grid, the ocean region definitions (called the region mask), and the ocean initial conditions. Optionally, the modeler may also specify new locations for diagnostic transport calculations. Other inputs to the ocean model are of the form of POP’s input_templates. These are files read into POP much like a namelist but deliver a wide variety of information.
Creating the ocean boundary forcing (grid, bathymetry, and region mask) are often time consuming and are subjective processes. In this section we give a general overview of the process followed by more detailed steps.
Tips on initial conditions choices and input template changes will be discussed in the detailed-steps sections.
The ocean bathymetry in POP is called the KMT. POP requires the ocean bathymetry (also referred to as ocean topography) to be input into the model as integer values that represent depth levels (not ocean depths). POP2 translates the depth levels into ocean depths using an ASCII file called the ‘vertical grid’ (e.g., gx1v6_vert_grid). The CESM1.1.1 vertical grid for the high (gx1v6) and low (gx3v7) resolution ocean grid specifies 60 vertical depth levels, (KMT=1-60). The vertical grid file has three columns that correspond to (1) ocean layer thickness (cm), (2) midpoint depth (m) of that layer, and (c) the actual depth of the layer (m). Each line of the vertical grid file equates to a KMT level; e.g., in the gx3v7 vertical grid file, KMT=2 equates to a layer thickness of 1000 cm, a midpoint depth of 15 m, and an actual layer depth of 20m. KMT=0 denotes land grid cells. We recommend using the default vertical grids.
depth of midpoint (m)
|actual layer depth (m)|
|5|| || || |
| || || || |
The paleoToolKit creates a KMT file based on your bathymetry data (contained in topobathy.nc) and place that data onto your model grid. Once the KMT data is placed onto the grid (both horizontal and vertical), the modeler will be required to edit the data to eliminate potential problems for the POP grid and miscellaneous errors generated by the automated process. Modifying the KMT is another subjective process, but we will provide some guidance.
a. Avoid one grid cell wide channels and bays at all levels. The ocean model will not be able to compute flow with one grid box. One typically removes these channels by filling them with land, or widening them to have a minimum width of two grid cell. Note, our tool contains an option to try and remove these channels automatically, but isolated points may still occur.
b. Channels that are not straight may contain a grid cell width of one where the channel curves (Figure 4). These transition areas will be missed with the automatic checks and must be edited. If not, there will be no flow through the transition area due to zero velocities at both corner (land) cell borders. The recommended change would be to widen the transition area to two ocean grid cells.
c. Avoid small and shallow bays. Although a two cell wide bay may contain ocean velocities in the middle of the bay, realistically, there may not be enough circulation to fully resolve the ocean flow. Widening these bays may avoid negative salinities (in the case of too much fresh water runoff into the bay) or super-saline bays (in the case of excess evaporation).
The region mask file is a simple binary file that assigns an integer number to each ocean basin. The integer value allows the ocean model to identify the various water bodies where the ocean model is active (lakes are handled in the land model and are considered land cells). For example, the modern oceans such as the Pacific, Atlantic, and Indian Oceans each have a unique region mask number. Enclosed active oceans, such as the Black Sea, are considered marginal seas and are identified as marginal with a negative integer number.
For deep time paleo cases, however, we may not have data to differentiate individual ocean basins, so we simplify the ocean region mask by dividing the domain into two regions: the Northern and Southern Hemispheres.
A simple tool to create your region mask file can be found in setup_tools.tar. This tool assumes your region mask file will contain only the Northern and Southern hemispheres. If this is not the desired mask, you will need to modify the Fortran code to specify your unique ocean regions.
Once regions have been chosen, the modeler will need to modify the ASCII input_template called the region_ids file to reflect the new regions.