This file describes the files in this directory used for running the ecosystem model on the mixed layer global grid described in the following two manuscripts. Please cite these papers as the source/reference for papers using this code.
Moore, J.K., Doney, S.C., Kleypas, J.A., Glover, D.M., Fung, I.Y., 2002a. An intermediate complexity marine ecosystem model for the global domain. Deep-Sea Res. II, 49: 403-462.
Moore, J.K., Doney, S.C., Glover, D.M., Fung, I.Y., 2002b. Iron cycling and nutrient limitation patterns in surface waters of the world ocean. Deep-Sea Res. II, 49: 463-508.
For the estimates of atmospheric iron deposition please reference the original source papers.
Tegen, I., Fung, I.Y., 1994. Modeling mineral dust in the atmosphere: Sources, transport, and optical thickness. J. Geophys. Res., 99: 22897-22914.
Tegen, I., Fung, I.Y., 1995. Contribution to the atmospheric mineral aerosal load from land surface modifications. J. Geophys. Res., 100: 18707-18726.
Mahowald, N., Kohfeld, K., Hansson, M., Balanski, Y., Harrison, S.P., Prentice, I.C., Schulz, M., Rodhe, H., 1999. Dust sources and deposition during the last glacial maximum and current climate: A comparison of model results with paleodata from ice cores and marine sediments. J. Geophys. Res., 104: 15895-15916.
For the other model input files, please cite the original data sources as cited in the Moore et al. papers.
Documentation
| a_documentation_1.0 | Draft documentation for running the model |
Model Code Files (download tar file jkmoore_code.tar)
| bio_2d_x3pV5.f | Main module of global mixed layer grid code |
| bio_subs_x3pV5.f | Main module of marine ecosystem model code |
| numerics_subs.f | Numerical code for implementing Runge-Kutta driver |
| biocommon_x3p.inc | Common variables for global mixed layer model |
| bioparam_x3pV5.inc | Parameters for global mixed layer model |
| MakefileV5 | Makefile to compile code |
Input Files - for Global Mixed Layer Model (download tar file jkmoore_inputs.tar)
| bio_slope_x3p_globalV5.dat | Slope vs. Depth file for nutrients, used in calculating bottom boundary conditions (see Documentation) |
| bio_surf_x3pV5.dat | Surface intercept used in calculating bottom boundary conditions (see Documentation). |
| bio0_x3p_oldV5.dat | Inital concentrations for ecosystem scalars. |
| fedepo_nmol_Maho_LGM_x3p.dat | Monthly surface iron deposition for the Last Glacial Maximum from Mahowald et al., 1999. (see model code for all flux units). |
| fedepo_nmol_Mahowald_x3p.dat | Monthly surface iron deposition for modern times from Mahowald et al., 1999. |
| fedepo_nmol_TegenFung_x3p.dat | Monthly surface iron deposition for modern times from Tegen and Fung 1994; 1995. |
| fice_1098_0999_x3p.dat | Monthly percent sea ice cover from satellite data for the period Oct.1998
- September 1999.
NOTE: DATA HAS BEEN REARRANGED SO FILE RUNS FROM JANUARY - DECEMBER. |
| hmix_levpd_min25_x3p.dat | Monthly mixed layer depth from the climatology of Monterey and Levitus, 1997. A minimum mixed layer depth of 25m has been prescribed. |
| hmix_levpd_x3p.dat | Monthly mixed layer depth from the climatology of Monterey and Levitus 1997. |
| input_x3p.bio_2dV5 | Main input file containing biological parameter values. |
| qsw_x3p.dat | Surface shortwave radiation. |
| woa98_sst_surf_m_x3p.dat* | Monthly average sea surface temperature (from World Ocean Atlas '98). |
| wturb_x3pV5.dat | Turbulent mixing rate at base of the mixed layer. |
| wvel_x2p_3x3_x3p.dat | Vertical velocity at the base of the mixed layer. |
| x3p_mask | Land mask for the global mixed layer grid. Land=0, Ocean>0.0 |
*Note (12 Mar 02) - The file woa98_sst_surf_m_x3p.dat was missing in the tar file prior to this date.
IDL Files (download tar file jkmoore_idl.tar)
| idl_global_budgetsV5.pro | Routine to sum annual fluxes from the model. |
| idl_limnutrientsV5.pro | Routine to map the limiting nutrient during summer months for each phytoplankton group. |
| idl_plot_both_export_x3p.run | Plots sinking export and total biogenic carbon export from the surface mixed layer. |
| idl_plot_caco3_both_x3p.run | Plots Calification and sinking CaCO3 export. |
| idl_plot_Nfix_x3p.run | Plots annual nitrogen fixation by the diazotrophs. |
| idl_prod_vgpm_x3p.run | Plots annual primary production from the mixed layer model and from the satellite-based estimate of the VGPM by Behrenfeld and Falkowski, 1997 model (see Moore et al. 2001b for details). |
| out_vgpm_x3p.dat | Contains production data from the VGPM, input file for idl_prod_vgpm_x3p.run |
| idl_seaw_x3p.run | Plots model predicted monthly mean chlorophyll concentration in comparision
with SeaWiFS data from the period October 1998 - Sept. 1999.
NOTE: DATA HAS BEEN REARRANGED SO FILE RUNS FROM JANUARY - DECEMBER. |
| seaw_1098_0999_log.dat | data file with seawifs data for idl_seaw_x3p.run |
| v5_init_bio_slope_x3p.run | Initializes the bio_slope_x3p_globalV5.dat file used in calculating bottom boundary conditions in the model. Uses a number of input files described below. |
| oceanarea_x3p.dat** | Provides ocean area in m^2 for each gridpoint. Used to calculate total mixed layer flux at each grid point |
| feno3_200_natl40_x3p.dat | Regional estimation of the ratio of dissolved fe to nitrate below the surface mixed layer from Fung et al., 2000 modified as described in Moore et al., 2001a. |
| no3_surf_summer_WOA98_5x5.dat | surface nitrate concentrations from the World Ocean Atlas 1998 remapped to our global grid and then smoothed with a 5x5 boxcar filter. |
| sio2_surf_summer_WOA98_5x5.dat | surface silicate concentrations from the World Ocean Atlas 1998 remapped to our global grid and then smoothed with a 5x5 boxcar filter. |
| po4_surf_summer_WOA98_5x5.dat | surface phosphate concentrations from the World Ocean Atlas 1998 remapped to our global grid and then smoothed with a 5x5 boxcar filter. |
| sio2_WOA98_x3p.dat | Depth resolved silicate fields from the World Ocean Atlas 1998 remapped to the NCAR x3prime grid (see Documentation). |
| no3_WOA98_x3p.dat | Depth resolved nitrate fields from the World Ocean Atlas 1998 remapped to the NCAR x3prime grid (see Documentation). |
| po4_WOA98_x3p.dat | Depth resolved phosphate fields from the World Ocean Atlas 1998 remapped to the NCAR x3prime grid (see Documentation). |
| x3p_depth | Depth levels of the NCAR x3prime ocean model grid. |
| smooth_x3p | IDL routine called by init_slope to smooth slopes with 3x3 boxcar. This routine is in the file x3p_routines.pro |
| v5_init_x3p_2d.run | This routine creates several input files used in the model |
| bio_surf_x3pV5.dat | used in the bottom boundary condition calculations |
| bio0_x3p_oldV5.dat | Initial concentrations of all ecosystem scalars. |
| wturb_x3pV5.dat | Turbulent mixing rate at base of mixed layer, currently a uniform rate of 0.15 m/day (see Moore et al., 2001a). |
| xt_3x3p | tracer long. values, used in some plotting routines |
| xu_3x3p | velocity long. values, used in some plotting routines |
| x3p_gridpoints | lat/long boundaries of global mixed layer gridpoints. |
| x3p_routines.pro | a number of IDL routines for manipulating model data. |
**Note (18 Mar 02) - The file oceanarea_x3p.dat was missing in the tar file prior to this date.