Updated to v.0.1.2

There was an issue with testing using matplotlib that has (hopefully) been fixed

…bolus velocity * temperature to eddy stats

…develop

Updated to v.0.1.3

…develop

Added monthly mean zonal and meridional bolus velocities as well as
bolus velocity times temperature to eddy stats for Labrador Sea bias/ GM
testing

Removes the vertical averaging of the GM kappa bolus diffusivity.
Testing shows this functionality is not beneficial to simulations

In the GM bolus calculation, there is a specified diffusivity and phase
speed (see Ferrari et al. 2010). Currently MPAS-O assumes these values
are fixed in time and space. This PR allows separate flags to enable
2D varying (+time) phase speed (based on the first baroclinic mode phase
speed) and a separate flag for 3D (+time) varying diffusivity.

Change order of default namelist to be: main; tracer groups; analysis members; init mode

…velop

* ocean/add_gm_to_compass_testing:
  Change order of default namelist and suggested COMPASS namelist
  Add GM flags to COMPASS global ocean test

…ssues

…elop

This PR fixes a threading issue that was introduced in [E3SM PR#3057]
(E3SM-Project/E3SM#3057) that brought in
the initial implementation of 3D varying GM bolus. After that commit,
some E3SM threading tests were observed to fail with different results.

Tested with:
* SMS_P12x2.T62_oQU240.CMPASO-NYF.compy_intel - BFB results 10 times
* SMS_P12x2.ne4_oQU240.A_WCYCL1850.compy_intel.allactive-mach_mods - BFB
* results 10 times

This last test is one that was failing on sandiatoss3.

Minor updates to MPAS framework. Includes:
- Log file corrections
- python 3 correction in COMPASS
- changes to atmospheric core

layerThickness pointer was passed into a subroutine but it is
unassociated, and never used in that subroutine. This causes an error
with Intel 19 compilers. This PR simply removes the unused variable.

This PR is an accumulation of PRs into the ocean/coastal branch. We are
bringing them in at once for efficiency:
 MPAS-Dev#285, MPAS-Dev#289, MPAS-Dev#284, MPAS-Dev#295, MPAS-Dev#310, MPAS-Dev#311, MPAS-Dev#312, MPAS-Dev#335, MPAS-Dev#354, MPAS-Dev#356, MPAS-Dev#358, MPAS-Dev#359,
 MPAS-Dev#365, MPAS-Dev#371

This fixes these:
1. The seg fault mentioned in
MPAS-Dev#374 (comment).
When we use:
`config_am_mocstreamfunction_normal_velocity_value =
'normalTransportVelocity'`
it tries to access from the 'state' var_struct rather than 'diagnostic'
here:
`496          call mpas_pool_get_array(statePool,
normalVelocityArrayName, normalVelocity, timeLevel)`
I propose that we always use 'normalTransportVelocity' here for all
simulations, and remove this flag.

2. The StrLen in the new MOC mask file is 1024 rather than 64. This
causes all string arrays to be read in as blank. In particular,
`transectGroupNames` and `regionGroupNames`, so a match is never found,
and `regionGroupNumber` and `transectGroupNumber` remain zero and can
cause a seg fault.  It appears StrLen=64 is hardwired within MPAS
framework, though I couldn't find it. The simple solution here is to
just use StrLen=64. On the current mask file:
`ncks -d StrLen,0,63 in.nc out.nc`

These three 3D variables are in the Registry, and one is obtained, but
none are used. Git blame shows they were added by Todd and Doug in 2013,
but then Qingshan Chen added his own naming scheme for GM.

This is a simple mistake that needs to be fixed. Causes a seg fault when
using more than three regions.