DOI: 10.5061/dryad.w3r228116
title: Data From: Ocean circulation, sea ice, and productivity simulated in Jones Sound, Canadian Arctic Archipelago, between 2003-2016

description: In this publication, we provide data and numerical model code associated
 with the manuscript "Ocean circulation, sea ice, and productivity
 simulated in Jones Sound, Canadian Arctic Archipelago, between
 2003-2016". In this study, we modeled ocean circulation, sea ice
 dynamics, and biological productivity within Jones Sound, high Canadian
 Arctic Archipelago, between 2003 and 2016, with a high resolution regional
 configuration of the Massachusetts Institute of Technology general
 circulation model (MITgcm). This data publication includes all MITgcm
 parameter files that are needed to run the regional Jones Sound ocean-sea
 ice-biological productivity model, all model boundary and initial
 conditions, and ocean model temperature and salinity depth-profiles used
 in validation. 
description: All model parameter files are in standard MITgcm format. All
 model boundary and initial conditions have been interpolated onto the
 regular model grid. 
description: # Data From: Ocean circulation, sea ice, and productivity dynamics
 simulated in Jones Sound, Canadian Arctic Archipelago, between 2003-2016
 [https://doi.org/10.5061/dryad.w3r228116](https://doi.org/10.5061/dryad.w3r228116) ## Description of the data and file structure The data provided in this publication include all MITgcm parameter files and initial/boundary conditions needed to run the regional Jones Sound, Canadian Arctic Archipelago, ocean-sea ice-biological productivity model between 2003-2016. All model parameter files are in MITgcm readable format (we used MITgcm checkpoint 66j). All model input data files are in binary format (.bin) and are also ready for use within MITgcm. Processed oceanographic profiles are provide as .mat files and can be accessed using MATLAB, whereas raw oceanographic profiles are provided as .txt files. ### Files and variables #### Compressed directory 1: ModelCode.zip **Contents:**  * data: Main MITgcm parameter file that contains continuous equation parameters, Elliptic solver parameters, time stepping parameters, output parameters, gridding parameters, and the file paths of input datasets. * data.#: MITgcm module parameter files where # is either bling (biological productivity module), cal (calendar module), diagnostics (model diagnostic outputs), exch2 (Extended Cubed Sphere Topology), exf (external forcing), gchem (biogeochemistry module), ggl90 (TKE vertical mixing scheme), kpp (Nonlocal K-Profile Parameterization for Vertical Mixing), obcs (open boundary condition parameters), ptracers (tracers for MITgcm to keep track of), and seaice (sea ice model parameters). #### Compressed directory 2: ModelData.zip **Contents:**  * Ocean Model Inputs: All ocean, sea ice, and biological productivity model inputs (excluding atmospheric forcing, which was taken from the Arctic Systems Reanalysis v2 and is publicly available). Note that the ocean model grid is of dimensions 840 x 156 x 70. * topo_840x156_eded.bin: Model bathymetey (840 x 156) * FOB#@.bin: Monthly ocean model boundary condition where # (N, S, E, or W) defines the North, South, East, or West open boundary, respectively, and @ (s, t, u, v, or eta) defines the variable included in the file (salinity, temperature, u-velocity, v-velocity, surface height). East/West boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * OB#@.bin: Monthly sea ice model boundary condition where # (N, S, E, or W) defines the North, South, East, or West open boundary, respectively, and @ (a, h, sl, sn, uice, vice) defines the variable included in the file (concentration, thickness, salinity content, snow depth, u-velocity, v-velocity). East/West boundary files are of dimension 156 x 169 and North/South boundary files are of dimension 840 x 169. * \#File.bin: Sea ice model initial conditions where # is Area (concentration), Heff (thickness), Salt (salinity content), and Snow (snow depth). The dimensions of each field are 840 x 156. * Theta.bin: Ocean model initial temperature field (840 x 156 x 70) * Salt.bin: Ocean model initial salinity field (840 x 156 x 70) * Uvel.bin: Ocean model initial u-velocity field (840 x 156 x 70) * Vvel.bin: Ocean model initial v-velocity field (840 x 156 x 70) * Heff.bin: Ocean model initial surface height field (840 x 156) * alk_init_glodapv2_jones.bin: Initial alkalinity conditions for biological productivity module (840 x 156 x 70) * alk_obc#_glodapv2_10yrsclim_jones.bin: Monthly alkalinity boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * dic_init_glodapv2_jones.bin: Initial dissolved inorganic carbon conditions for biological productivity module (840 x 156 x 70) * dic_obc#_glodapv2_10yrsclim_jones.bin: Monthly dissolved inorganic carbon boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * don_init_blingv2_jones.bin: Initial dissolved organic nitrogen conditions for biological productivity module (840 x 156 x 70) * don_obc#_blingv2_10yrsclim_jones.bin: Monthly dissolved organic nitrogen boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * dop_init_blingv2_jones.bin: Initial dissolved organic phosphate conditions for biological productivity module (840 x 156 x 70) * dop_obc#_blingv2_10yrsclim_jones.bin: Monthly dissolved organic phosphate boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * fe_init_blingv2_jones.bin: Initial iron conditions for biological productivity module (840 x 156 x 70) * fet_surfflux_mahowald_jones.bin: Surface flux of iron (840 x 156) * fe_obc#_blingv2_10yrsclim_jones.bin: Monthly iron boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * no3_init_woa18_jones.bin: Initial nitrate conditions for biological productivity module (840 x 156 x 70) * no3_obc#_woa18_10yrsclim_jones.bin: Monthly nitrate boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * o2_init_woa18_jones.bin: Initial oxygen conditions for biological productivity module (840 x 156 x 70) * o2_obc#_woa18_10yrsclim_jones.bin: Monthly oxygen boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * po4_init_woa18_jones.bin: Initial phosphate conditions for biological productivity module (840 x 156 x 70) * po4_obc#_woa18_10yrsclim_jones.bin: Monthly phosphate boundary conditions where # is n, s, or e (north, south, or east boundary, respectively). East boundary files are of dimension 156 x 70 x 169 and North/South boundary files are of dimension 840 x 70 x 169. * phyto#_init_blingv2_jones.bin: Initial phytoplankton conditions where # is Diaz (Diazotrophs), Lg (large), or Sm (small) (840 x 156 x 70). * si_surf_clim_woa18_jones.bin: Initial surface silicate conditions (840 x 156 x 70) * Validation: * MitCasts: Modeled vertical temperature/salinity profiles using MITgcm output. Contains MATLAB files #@.mat where # (T or S) defined temperature or salinity profile and @ (102, 108, 323, Bel, JS) defines the station where the profile is extracted from. ## Missing Values Note that missing values (indicated by NaNs) are present in the modeled temperature and salinity-depth profiles. We provide these profiles down to the deepest ocean model grid level; however, it is often the case that the bathymetry is shallower than that level. Thus, we use NaNs indicate that no ocean data is present (i.e., that the profile is deeper than the bathymetry) at the selected levels. ## Code/software All model parameter files are developed to run with the Massachusetts Institute of Technology general circulation model (MITgcm; checkpoint 66j). All model input and boundary conditions can be loaded with the MITgcm tool readbin(), which is written in MATLAB. For example, if we wanted to read in Theta.bin and store the data in a variable called "T", we would use the following command: T = readbin('Theta.bin',[840 156 70]), where the second input into the function is the size of the output field. In addition, all processed oceanographic profiles are provided as *.mat files and can be read using MATLAB. ## Access information Other publicly accessible locations of the data: * MITgcm (including the sea ice and productivity modules) is available for download at [https://mitgcm.org.](https://mitgcm.org) * Amundsen Ice Breaker oceanographic profiles are publicly available for download through the Polar Data Catalogue ([https://amundsenscience.com/data/data-access/](https://amundsenscience.com/data/data-access/)) * Arctic Systems Reanalysis v2 dataset (model atmospheric forcing) is available through the UCAR data portal ([https://rda.ucar.edu/datasets/ds631.1/](https://rda.ucar.edu/datasets/ds631.1/)) * Canadian sea ice charts covering the Eastern Arctic are publicly available through the National Snow and Ice Data Center ([https://nsidc.org/data/g02171/versions/1](https://nsidc.org/data/g02171/versions/1))