Pyticles is a Python/Fortran hybrid parallelized code for Lagrangian particles 3D advection from high-resolution ROMS/CROCO model data.

• Gula, J., M.J. Molemaker & J.C. McWilliams, 2014 : Submesoscale cold filaments in the Gulf Stream, J. Phys. Oceanogr., 44, 2617-2643.
• Vic, C., G. Roullet, X. Carton, X. Capet, M.J. Molemaker & J. Gula, 2015 : Eddy-topography interactions and the fate of the Persian Gulf Outflow, J. Geophys. Res. Ocean., 120, doi :10.1002/2015JC011033.
• Gula, J., M.J. Molemaker & J.C. McWilliams, 2016 : Submesoscale dynamics of a Gulf Stream frontal eddy in the South Atlantic Bight, J. Phys. Oceanogr., 46, 305-325.
• Klymak, J.M., R.K. Shearman, J. Gula, C.M. Lee, E.A. D’Asaro, L. Thomas, R. Harcourt, A. Shcherbina, M.A. Sundermeyer, M.J. Molemaker & J.C. McWilliams, 2016 : Submesoscale streamers exchange water on the North Wall of the Gulf Stream, Geophys. Res. Lett., 43, 1226–1233.
• Ramanantsoa, J.D., M. Krug, P. Penven, M. Rouault & J. Gula, 2018 : Coastal upwelling south of Madagascar : temporal and spatial variability, Journal of Marine System, 178, 29-37.
• Ramanantsoa, J.D., P. Penven, M. Krug, J. Gula & M. Rouault, 2018 : Uncovering a new current : the South-west MAdagascar Coastal Current (SMACC), Geophys. Res. Lett., 45, 1930-1938, doi :10.1002/2017GL075900.
• Ragoasha, N., S. Herbette, G. Cambon, J. Veitch, C. Reason, C. Roy, 2019: Lagrangian pathways in the southern Benguela upwelling system, Journal of Marine Systems, 195, 50-66, https://doi.org/10.1016/j.jmarsys.2019.03.008.
• Gula, J., T. Blacic, & R.E. Todd, 2019 : Submesoscale coherent vortices in the Gulf Stream, Geophys. Res. Lett., 46, 2704-2714. https ://doi.org/10.1029/2019GL081919
• Smilenova, A., J. Gula, M. Le Corre, L. Houpert & Y. Reecht, 2020 : A persistent deep anticyclonic vortex in the Rockall Trough sustained by anticyclonic vortices shed from the slope current and wintertime convection, J. Geophys. Res. Ocean, https ://doi.org/10.1029/2019JC015905.
• Vic, C., S. Hascoet, J. Gula, T. Huck, & C. Maes, 2022 : Oceanic mesoscale cyclones cluster surface Lagrangian material, Geophys. Res. Lett, 49, e2021GL097488. https ://doi.org/10.1029/2021GL097488.
• Wang, L., J. Gula, J. Collin & L. Memery, 2022 : Effects of mesoscale dynamics on the distribution and transport of gravitationally sinking particles to the deep ocean, J. Geophys. Res. Ocean, 127, e2022JC018799. https://doi.org/10.1029/2022JC018799
• Qu, L., L. Thomas, A. Wienkers, R. Hetland, D. Kobashi, J. Taylor, F. Hsu, J. MacKinnon, R. Shearman, J. Nash, 2022 : Rapid Vertical Exchange at Fronts in the Northern Gulf of Mexico, Nat Commun. 13, 5624, https://doi.org/10.1038/s41467-022-33251-7
• Tagliabue, A., A. Lough, C. Vic, V. Roussenov, J. Gula, M. Lohan, J. Resing, & R. Williams, 2022 : Mechanisms driving the dispersal of hydrothermal iron from the northern Mid Atlantic Ridge, Geophys. Res. Lett., https://doi.org/10.1002/essoar.10512044.1
• Ragoasha, N., S. Herbette, J. Veitch, G. Cambon,C. Reason, C. Roy, 2022: Inter-Annual Variability of the Along-Shore Lagrangian Transport Success in the Southern Benguela Current Upwelling System, J. Geophys. Res. Oceans, 127, e2020JC017114, https://doi.org/10.1029/2020JC017114
• Picard, T., J. Gula, R. Fablet, J. Collin & L. Memery, 2024 : Predicting particle catchment areas of deep-ocean sediment traps using machine learning, Ocean Sci., 20, 1149–1165,https://doi.org/10.5194/os-20-1149-2024
• Picard, T., J. Gula, C. Vic & L. Memery, 2024: Seasonal tracer subduction in the Subpolar North Atlantic driven by submesoscales, J. Geophys. Res. Oceans, 129, e2023JC020782. https://doi.org/10.1029/2023JC020782
• Wang, L., J. Gula, J. Collin, L. Memery & X. Yu, 2025: Connecting the deep collection of sinking particles with surface ocean signatures, J. Geophys. Res. Oceans, in press
• Picard, T., C. Baker, J. Gula, R. Fablet, L. Memery & R. Lampitt, 2025: Estimating the variability of deep ocean particle flux collected by sediment traps using satellite data and machine learning, Biogeosciences, https: //doi.org/10.5194/egusphere-2024-3292.

The latest release has been archived on zenodo:

• netcdf4
• gfortran
• conda

git clone https://github.com/Mesharou/Pyticles.git

cd Install/
conda env create -f conda_install.yml

tcsh users:

module load anaconda-py3.6/4.7.12

create new env

conda create --name pyticles

conda init tcsh
conda activate pyticles

install modules

conda install numpy
conda install scipy
conda install matplotlib
conda install netCDF4

bash users:

module load conda/latest
module load NETCDF/4.3.3.1-mpt-intel2016

cd Install/
conda env create -f conda_install.yml

cd Modules/
make all

All Pyticles parameters and options are defined in Inputs/input_file.py

You must define a simulation name and modify Modules/R_files.py accordingly to set the croco file's path

To run Pyticles sequentially (interactively)

python -i Pyticles.py 1 

In parallel with $np OpenMP procs

python Pyticles.py $np > out