Add three bedload transport formulae and four sediment fall velocity formulae

Bedload transport formulae
- Soulbsy-Damgaard [2005]
- Meyer-Peter-Meuller [1948]
- Engelund-Hansen [1967]
Sediment fall velocity formulae
- Goldstein-Coco2013
- VanRijn1993
- Soulsby1997
- Cheng1997

Add Manning equation to calculate Chezy roughnes coefficient
in Engelund-Hansen bedload formula.

The Manning equaiton reads:
Chezy = 1/Manning*(bottomDepth)^(1/6)
Chezy value is manually restricted between [20 ,100]

Add suspended sediment concentration (SSC) algorithms

SSC is solved by bottom reference concentration and Rouse profile
Bottom reference concentration is computed by one of the following formulae
- Lee et al., 2004
- Goldstein et al., 2014
- Zyserman-Fredsoe 1997
Rouse profle assumes the eddy diffusivity to vary parabolically with height

Fixed bugs in calculations of SSC and theta in sediment_transport.F

Fixed two bugs in mpas_ocn_sediment_transport.F

- Corrected SSC Rouse profile equation
  The old equation from Page 138 of Soulsby's book "Dynamics of Marine
  Snads" (1997) is wrong. The right equation(s) can be found in
  (1) van Rijn 1984: Sediment Transport, Phase II: Suspended Load
  Transport. J. Hydraul. Eng.
  (2) Wang 2012: Measuring and Modeling Suspended Sediment Concentration
  Profile in the Surf Zone. Marine Sedimentology
- Corrected z-coordinate calculation
  The global variable zMid is zero at surface and negative downward. The
  water depth from bottom z was mistakely set to -zMid. Now the calculation
  is z=ssh+bottomDepth+zMid

Fixed a bug in mpas_ocn_sediment_transport.F

zMid is the distance from the mean surface layer, with positve upward.
So for each vertical layer center, the distance above the sea bottom is
bottomDepth+zMid, which was wrongly set as ssh+bottomDepth+zMid in the
last commit.

Replaced Rouse profile equation by van Rijn's equations; modified xml
files to output ssh, mesh and velocity in sediment transport output file.

Mannually set a maximum value for Rouse number to avoid "Float-point
exception" error; fixed a bug in the implementation of
'Zyserman-Fredsoe1994' equation.

…coastal

This PR adds sediment transport analysis member (Phase I) to the model,
with the following variables computed:
- sediment settling velocity
- sediment erosion flux
- sediment bedload transport flux
- suspended sediment concentration in water column

Adds examples of JIGSAW workflow for coastal cases.
  Adds HI refined case
  West coast mesh from SF to LA

This currently only affects coastal test cases.

This should let us set $CARTOPY_DIR in a compass activation
script on LANL IC

Fixes analysis script based on new xarray api

…ean/coastal

Near as I can tell, this script is not used and the test case works
without it.

closes MPAS-Dev#431

Adds spatially-variable Cd and Mannings n drag
capabilities.

Adds comparison of different use for Cd:
ocean/drying_slope/zstar_variableCd/1km

Adds variable Manning's n drying slope:
ocean/drying_slope/zstar_variableManningn/1km

Adds spatially variable drag coefficient capability
based on Cd and n.

Fix cartopy issues with tricontourf

Refractors the zstar test case to allow for above-land wetting/drying.

…above_land

Refractors the zstar test case to allow for above-land wetting/drying in a new test case.

 * Adds drying slope wetting and drying above land

Switch COMPASS from basemap to cartopy

 - Add missing +1 offset to cell IDs used in the points.nc file
   generated in the init step of the hurricane Sandy cases.

…oastal

Fix bug in pointwiseStats locations for Sandy cases

Simple 0 vs 1 offset error

 - Includes the hurricane_wind_pressure code from Donatella Pasqualini
   that interpolates a parametric wind field onto the MPAS-O mesh

 - New test case (ocean/hurricane/USDEQU120at30cr10rr2/synthetic_sandy)
   includes a tidal spin-up period before the storm winds begin.

   This is needed because the storm winds only cover a 3 day period prior to
   landfall (not enough time to spin-up tides accurately)

 - Also, adds the ability to delay the ramp for the atmospheric forcing.
   In this case this is used to delay the wind/pressure forcing ramp until
   after the tidal spin-up.

…s_implicitCd into ocean/coastal

Fixes implicitCd computation bug in mpas_ocn_vmix.F

Previously we missed a factor of 0.5 within parentheses, which will slightly boost
Cd by a factor of approximately 2.5, to increase drag felt in simulation for a given
Manning's n value.