From 93192b9899004fcc298966e5323bb960ef66e5a8 Mon Sep 17 00:00:00 2001 From: Hannah Klion Date: Thu, 12 Dec 2024 18:29:32 -0800 Subject: [PATCH] Update paper.md --- paper/paper.md | 53 +++++++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 5d12c52..1a94893 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -44,7 +44,7 @@ affiliations: - name: Argonne National Laboratory index: 3 -date: March 2024 +date: January 2025 bibliography: paper.bib --- @@ -67,41 +67,44 @@ through the Science Discovery through Advanced Computing (SciDAC) partnership pr # REMORA Features -### Evolution Equations +### Hydrodynamic Evolution -REMORA solves the ... -and incorporates temperature, salinity, and an arbitrary scalar which can be advected and diffused. - -### Turbulence/Mixing Schemes +REMORA solves the incompressible time-dependent Navier-Stokes equation with the Boussinesq and hydrostatic approximations. +Temperature, salinity, and a passive scalar are also advected and diffused. +The density is calculated from a linear equation of state. The strength of vertical diffusion and viscosity is parametrized either by a spatially-varying analytical function or a Generic Length Scale (GLS) model. ### Time and Space Discretization and Terrain -The time discretization in REMORA is the ... model as described on ROMS web page. -In each time step, the depth-averaged equations are first advanced to determine mean quantities -and ocean height, then the full three-dimensional equations are evolved for velocity and scalars. +Like ROMS, REMORA uses a split-explicit time-stepping scheme, where several fast barotropic (2D) steps take place within each baroclinic (3D) update. +In the barotropic steps, the code solves depth-averaged versions of the 3D evolution equations. +These vertically-averaged solutions are used to calculate the sea surface height and vertical-mean velocity. +Full 3D equations are then evolved for for velocities and scalars. +Specifically, REMORA uses the same time integration as Rutgers ROMS. +That is, each barotropic step consists of a leapfrog predictor followed by a three-time Adams-Moulton corrector. +The 3D momenta are updated with a third-order Adams-Bashforth scheme, and scalars are advanced with a leapfrog step with a trapezoidal correction. The spatial discretization in REMORA uses the classic Arakawa C-grid with scalar quantities at cell centers and normal velocities at cell faces. -Bathymetry is included in the discretizations as described here. - -For simulations over complex bathymetry ... -The model includes capability for application -of some common map projections (e.g., Lambert Conformal, Mercator). -The advection terms may be calculated using second- through sixth-order accurate +Bathymetry and sea-surface height are defined at the centers of the cells of the 2D grid. +Horizontally, the evolution equations are discretized over a boundary-following, orthogonal curvilinear grid, specified by metric terms. +This formulation allows for grids that, for example, conform to coastlines. +Land areas can be included in the domain and are represented by masks on cell centers and edges. +Fluxes, velocities, and tracer values are set to zero where the land mask is true. +The advection terms may be calculated using second- through fourth-order accurate spatial discretizations, including both centered difference and upwind schemes. -### Dynamic and Static Mesh Refinement - -REMORA supports both static and dynamic (adaptive) mesh refinement, -with subcycling in time at finer levels of refinement. +Vertically, the domain is discretized using a stretched, terrain-following vertical coordinate. +There are the same number of vertical levels everywhere; a spatially-varying water column depth (bathymetry and sea-surface height) is captured by cells of different thickness. +Cell thicknesses are determined by a non-linear transformation function that has parameters to control the distribution of levels. ### Physical Forcings and Boundary Conditions -Physical forcings include Coriolis and wind stress forcing. +Physical forcings include Coriolis, wind stress forcing, and bottom drag. Lateral boundary conditions can be specified as periodic, inflow/outflow, -or time-varying values read in from external files in netcdf format. -The initial data can be specified by the user or read in from netcdf files. +or time-varying values read in from external files in NetCDF format. +The solution at the boundary can either be clamped to the value specified from file or incorporated by a nudging scheme. +The initial data can be specified by the user analytically or read in from NetCDF files. # Statement of need @@ -121,12 +124,14 @@ evolve. # Acknowledgements Funding for this work was provided by the U.S. Department of Energy -Office of Energy Efficiency and Renewable Energy Wind Energy Technologies Office. +Office of Science. We acknowledge the help of the AMReX team -in developing and supporting new AMReX features needed by ERF. +in developing and supporting new AMReX features needed by REMORA. The work at LBNL was supported by the U.S. Department of Energy under contract No. DE-AC02-05CH11231. The work at PNNL was supported by the U.S. Department of Energy under contract No. +The work at ANL was supported by the U.S. Department of Energy +under contract No. # References