Idealized hydrodynamical numerical model dataset with no-river runoff at the western tropical North Atlantic

The western tropical North Atlantic (WTNA) is a very complex region, with the influence of intense western boundary currents in connection with equatorial zonal currents, important atmospheric forcings (e.g Intertropical Convergence Zone), mesoscale activities (e.g NBC rings), and the world’s largest river discharge as the Amazon River runoff. The volume discharge is equivalent to more than one-third of the Atlantic river freshwater input, with a plume that spreads over the region reaching the northwestward Caribbean Sea and eastward longitudes of 30°W, and influencing from physical to biological structures. Therefore, in order to enable and encourage more understanding of the region, here we present a dataset based on an idealized scenario of no river runoff of the Amazon River and Par ´a River in the WTNA. The numerical simulations were conducted with a regional oceanic modeling system (ROMS) model and three pairs of files were generated with the model outputs: (i) ROMS-files, with the parameters of the ROMS-outputs raw data in a NetCDF format and monthly and weekly frequencies; (ii) MATLAB-files, which contain oceanographic parameters also in monthly and weekly frequencies; and (iii) NetCDF-files, with oceanographic parameters again in monthly and weekly frequencies. For each file, we present the coordinates and variable names, descriptions, and correspondent units. The dataset is available in the Science Data Bank repository (doi: https://doi.org/10.57760/sciencedb.02145)


Introduction
The western tropical North Atlantic (WTNA) is characterized as an extremely complex region with the influence of different physical forcings, such as strong western boundary currents (e.g.North Brazil Undercurrent and North Brazil Current) in connection with zonal equatorial currents (e.g South Equatorial Undercurrent, Equatorial Undercurrent, and North Equatorial Countercurrent) as part of the equatorial current system 1 ; important atmospheric drivers (e.g trade winds and the Intertropical Convergence Zone) 2 ; and mesoscale activity (e.g NBC rings) 3,4 .Besides, the region also presents an important pathway of interhemispheric transport of mass, heat, and salt as part of the Atlantic Meridional Overturning Circulation 5,6 .
A singular aspect of this region is the presence of the Amazon River runoff, the world's largest river discharge accounting for 18% of the continental water flow to the oceans and approximately 32% of the freshwater input to the Atlantic ocean, with an average of 222,800 m 3 s −17,8 .The discharge volume reaches up to two-fold the net atmospheric freshwater flux (evaporation-precipitation) over the WTNA 9 .Furthermore, the Amazon River forms a plume over the region, which extends over a thousand of kilometers, flowing northwestward and reaching the Caribbean Sea and also retroflecting eastward through the North Equatorial Countercurrent and reaching latitudes of 30°W 10,11 .Therefore, the region is marked by an intense land-ocean synergy, with several processes in play, such as mixed layer depth changes and formation of barrier layers, leading variations of the ocean surface heat balance 12,13 ; high terrestrial sediments and dissolved organic matter transport 11 ; and complex and important biogeochemical interactions, from nutrient and carbon fluxes 14,15 to changes on biological community structures 16 .
The present work brings a dataset originated from simulations using the regional oceanic modeling system (ROMS) model in an idealized scenario of no river runoff of the Amazon River and the Pará River in the WTNA.The main goal for the creation of the here presented dataset is to enable and encourage the development of more researches in the region to advance in bridging the knowledge gaps of a such complex area.In the following Sections, we present the methods, which introduces the study area and explains the model configuration, the initial and boundary parameters; the dataset, with the directory structure of the dataset, the generated files, and details of the coordinates and variables of each of the generated files; and lastly, the data availability.

Methods
This study was conducted through ideal simulations with the ROMS numerical model, using the ROMS-AGRIF version (regional ocean modeling system -adaptive grid refinement) [17][18][19][20] , which has been successfully tested in the WTNA, specifically off the North and Northeastern Brazilian coast 12,[21][22][23][24][25][26][27][28][29][30][31] .The geographic localization of this dataset is 60.5°-24°W/5°S-16°N, which is illustrated in Figure 1 with the monthly sea surface temperature (SST) horizontal distribution in the period maximum Pará River runoff (March-April) and maximum Amazon River runoff (May-June) 7 .In these four months, the minimum SST found in the area corresponding to this dataset is 35 psu (practical salinity unit), with values reaching 32 psu over the river plume and 27 psu off the Amazon River mouth 29 .
For our simulation, all initial and boundary parameters have been spatially discretized at a horizontal resolution of 0.25° with non-isotropic grid from Earth Topography v2 (ETOPO2) bathymetry 32 and vertically using the sigma coordinate system (32 vertical levels).In the configuration file (ROMSTOOLS; romstools_param.m),ROMSTOOLS is a set of Octave compatible Matlab functions used to perform pre-processing of ROMS model input data, we used theta_s = 6 and theta_b = 0 (These two parameters indicate to the ROMS model how it has to consider the distribution of vertical levels near the surface and the bottom, both must take values between zero and seven, the higher the values of these, the more vertical levels will be concentrated near the surface and the bottom) 19,33 , obtaining 12 and 20 levels in the first 100m and 500m depth, respectively.Other parameters used in the grid discretization are: hc = 5.0, hmin = 150, hmax_coast = 500, hmax = 5000, rtarget = 0.25 (slope), and Roa = 85e3.Since tidal influence is important for the seawater mixing process in the surface layers, tides have been taken into account in our simulation and data were obtained from OSU TPXO7 Tide model 34,35 .The North, South, East and West lateral boundaries were considered open and the sea surface salinity (SSS) and sea surface temperature (SST) values for initial and boundary conditions were restricted to monthly mean values obtained from the World Ocean Atlas 2009 (WOA2009 dataset) 36,37 .For the surface forcing, it was used monthly climatology of the Comprehensive Ocean-Atmosphere Data Set (COADS05 dataset) 38 .This dataset is the last year of the numerical output (roms_his.ncand roms_avg.nc)

Dataset
The idealized hydrodynamical numerical model database with no-river runoff in the Northern and Northeastern Brazilian coast (IHMD-NRF) is the result of a research carried out by 29.As shown in Table 1, the dataset includes three pairs of files: (i) ROMS-files as two files in ROMS NetCDF format, containing the monthly and weekly numerical output (raw data); (ii) MATLAB-files as two files processed and converted in Matlab; and (iii) NetCDF-files as two more files also processed and converted in NetCDF standard format with mNC tool 39 , the file pairs in (ii) and (iii) are identical to (i), but have been converted to Matlab formats (they can be read in Octave, R and Python) and the NetCDF standard.For each file, some metadata were added using freeware tools called Climate Data Operator (CDO) 40 and NetCDF Operators (NCO) 41 .All files are organized in the directory structure shown in Figure 2.
The ROMSfiles directory stores the ROMS model numerical output files for monthly and weekly data for the 11 th year.
The outputs' dimensions, their description and dimension size are listed in Table 2.The parameter time does not need any conversion when working with MATLAB, the function datestr provides the date.The monthly output is dated on the first day of each month, while the weekly output is on the 4 th , 12 th , 19 th and 27 th of each month.The year of this date is relative to the simulation year, so it will always be 0011 (11 th year).Table 2 shows the time parameter twice, once at monthly and once at weekly frequency, corresponding to each of the ROMS-files outputs.In the monthly output file (rooms_ his_Y11.nc),there are 13 values because January -year 0012 is also included.
The current velocity component (vector) grids have 184 × 160 nodes, while the scalar parameter grids have 185 × 161 nodes.Still for the ROMSfiles, Table 3 shows all the variables, which are related to the oceanographic and surface physical parameters.Other complementary descriptions of the ROMS model output files, i.e ROMS-files, can be found in 42, 43.All the ROMS model output files that are in the directory can be visualized with the tools that are in the directory called Roms_tools/Visualization_tools/.The folder is a component of ROMSTOOLS, the main script is roms_gui and it is a graphical user interface (GUI) 19,33 .This GUI is developed in MATLAB GUIDE (Octave-compatible), so it allows you to reuse other functions to retrieve parameters at a given level or depth, or even at a specific coordinate or date, e.g.: get_var.m.The two pairs of files, i.e MATLAB-files and NetCDF-files, contain oceanographic parameters such as salinity, temperature, sea currents, sea surface height (SSH), seawater density, and vorticity (Table 4 and Table 5).Here we present the descriptions of the oceanographic parameters in standard MATLAB and NetCDF formats (stored in the MATLABfiles  and NetCDFfiles directories, respectively), all these files can be read in ncview, Panoply, CDO, NCO and other freewares like Octave, R and Python.In both cases, the time parameter has dimension size of 12 for each month of the 11 th year of the monthly simulation and it also presents dimension size of 48 for the weekly simulation, with output on the same dates as the equivalent files in NetCDF ROMS format (ROMS-files).In these four pairs of files, the vector and scalar data grids are referenced with the same coordinate system.
The standard NetCDF files, i.e NetCDF-files, are self-describing as it is possible to explore a very detailed description of the metadata with the ncdump command in terminal 44 .You  This data note presents a dataset "originated from simulations using the regional oceanic modeling system (ROMS) model in an idealized scenario of no river runoff".The study mainly conducted from modeling products aims to provide a database of oceanographic parameters useful for studies of the dynamics of the complex western tropical North Atlantic (WTNA) Ocean.The methods and materials provided all the information needed to reproduce this simulation.This dataset could be used for comparative studies to analyze the influence of the Amazon River runoff, the world's largest river discharge particularly in biogeochemistry and on ocean-atmosphere interactions.This database is a welcome addition.The report is well written, the figures are clear.Nevertheless, I suggest a few changes that should improve this data note.
Minor Comments:

Methods section:
In CROCO is a free surface model; therefore the model conserves the total mass of salt in the ocean so as to control the salinity in the model.It is an idealized scenario of no-river runoff but I suggest inserting few words about the salinity "recall".

Methods section:
Lines 7 "which is illustrated in Figure 1 with the monthly sea surface temperature (SST) horizontal".There is a mistake.It is not sea surface temperature but sea surface salinity.Reviewer Expertise: Physical Oceanography, Numerical modeling (CROCO), ocean-atmosphere interactions, biogeochemistry.
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
is proposed and allows the reproduction of the experiment.I only suggest that it be inserted in the methodology which tidal components were used in the simulation.Furthermore, everything is well placed and there are no questions.
I tested the files to verify if everything that was described is working properly.And yes, everything is perfect.Therefore, my recommendation is that it be indexed.
Is the rationale for creating the dataset(s) clearly described?Yes Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Physical Oceanography, Numerical modeling, ocean-atmosphere interactions, I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 1 .
Figure 1.Geographic location of the dataset.Sea Surface Salinity field in the periods of maximum Pará River runoff (March-April, upper panels) and maximum Amazon River runoff (May-June, lower panels).

Figure 2 .
Figure 2. Distribution of files by directory according to their format.

○ References " 21 .○
Silva AC, Bourles B, Araujo M: Circulation of the thermocline salinity maximum waters off the northern brazil as inferred from in situ measurements and numerical results.Ann Geophys.2009; 27(5): 1861-1873."Pleaseadd the circumflex accent "Bourlès".Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.

Table 5 . NetCDF-files variables (oceanographic parameters) contained in the NetCDFfiles directory.
can also preview the data using the ncview command in terminal45, GrADS 46 and Panoply data viewer 47 , the latter depending on the Java Runtime Environment.

and carbon fluxes in the estuaries of major rivers flowing into the tropical atlantic
. Front Mar Sci.2014; 1: 10.Publisher Full Text 16.Stukel MR, Coles VJ, Brooks MT, et al.: Top-

method for computing horizontal pressure- gradient force in an oceanic model with a nonaligned vertical coordinate.
J Geophys Res Oceans.2003; 108

and hydrodynamical structures within the deltaic regions and continental platforms adjacent to two northeastern Brazilian rivers.
Reg Stud Mar Sci.2022; 51: 102219.

tool for oceanographers and meteorologists to easily create their netcdf files using matlab. Zenodo
. 2021.

Analysis of self-describing gridded geoscience data with netCDF
Publisher Full Text 47. Fouilloux A: Visualize climate data with panoply netcdf viewer.2023.Reference Source What about the spin-up?Why did you choose the ROMS-model simulation of 11 years?Can you give more arguments to justify your choice?
the text "This dataset is the last year of the numerical output (roms_his.ncand roms_avg.