Merge pull request #316 from seahorce-scidac/paper

Update paper.md

paper/paper.md

@@ -78,25 +78,24 @@ The density is calculated from a linear equation of state. The strength of verti
 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. 
+Full 3D equations are then advanced to calculate depth-dependent velocities and scalars (temperature, salinity, etc.). 
 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 3D velocities 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 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.
+Horizontally, the evolution equations are discretized over a boundary-following, orthogonal curvilinear grid, which is 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.
+Land areas can be included in the domain and are represented by masks on cell centers and faces; fluxes, velocities, and tracer values are set to zero on land.
 The advection terms may be calculated using second- through fourth-order accurate
 spatial discretizations, including both centered difference and upwind
 schemes.
 
 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.
+There are the same number of vertical levels everywhere in the domain; a spatially-varying water column depth (bathymetry and sea-surface height) is captured by cells of different thickness.
+Cell thicknesses are determined by non-linear transformation and stretching functions that has parameters to control the distribution of levels.
 
 ### Physical Forcings and Boundary Conditions