added rst doc for Overview section 1.2 (including all figures) and changed chapter ordering

Author: Jeffery Scott

doc/index.rst

@@ -12,8 +12,8 @@ Welcome to MITgcm's user manual
    :numbered: 4
 
    overview/overview
-   phys_pkgs/phys_pkgs
    getting_started/getting_started
-   examples/examples
    contributing
+   examples/examples
+   phys_pkgs/phys_pkgs
    zreferences

doc/overview/bound_forc_inter_waves.rst

@@ -0,0 +1,20 @@
+
+Boundary forced internal waves
+------------------------------
+
+
+The unique ability of MITgcm to treat non-hydrostatic dynamics in the
+presence of complex geometry makes it an ideal tool to study internal wave
+dynamics and mixing in oceanic canyons and ridges driven by large amplitude
+barotropic tidal currents imposed through open boundary conditions.
+
+:numref:`slope_TU` shows the influence of cross-slope topographic variations on internal wave breaking - the cross-slope velocity is in color, the density contoured. The internal waves are excited by application of open boundary conditions on the left. They propagate to the sloping boundary (represented using MITgcm's finite volume spatial discretization) where they break under nonhydrostatic dynamics. 
+
+
+  .. figure:: figs/TUt8000slopecrop.*
+    :width: 80%
+    :align: center
+    :alt: slope_TU
+    :name: slope_TU
+
+    Simulation of internal waves forced at an open boundary (on the left) impacting a sloping shelf. The along slope velocity is shown colored, contour lines show density surfaces. The slope is represented with high-fidelity using lopped cells.

doc/overview/cvct_mixing_topo.rst

@@ -0,0 +1,25 @@
+Convection and mixing over topography
+-------------------------------------
+
+
+Dense plumes generated by localized cooling on the continental shelf of the
+ocean may be influenced by rotation when the deformation radius is smaller
+than the width of the cooling region. Rather than gravity plumes, the
+mechanism for moving dense fluid down the shelf is then through geostrophic
+eddies. The simulation shown in :numref:`fig_convect_and_topo`
+(blue is cold dense fluid, red is
+warmer, lighter fluid) employs the non-hydrostatic capability of MITgcm to
+trigger convection by surface cooling. The cold, dense water falls down the
+slope but is deflected along the slope by rotation. It is found that
+entrainment in the vertical plane is reduced when rotational control is
+strong, and replaced by lateral entrainment due to the baroclinic
+instability of the along-slope current.
+
+  .. figure:: figs/plume.*
+    :width: 70%
+    :align: center
+    :alt: Finit volume techniques
+    :name: fig_convect_and_topo
+
+    MITgcm run in a non-hydrostatic configuration to study convection over a slope.
+