add make_topo scripts to generate topography files on BC

[weiyuan-jiang]

Add make_topo scripts to generate topography files on BC.

PR needs this topo branch to work for stretched grids:
GEOS-ESM/Topo#1

[biljanaorescanin]

Summary of code testing:
In general most runs will finish in less then 1h but c90, c2160 and c2880 need ~3h. Since segments for overlap weights are dynamically determined runs will not be zero diff to itself but roundoff. Why we have different results for regular grid to before? I've implemented Girard formula with bounds checking which computes angles more accurately.

@wmputman do these numbers look OK to you? All verification on my side global plots/zoom in plots look ok. I've created a directory you can use to test to see do output files behave as you expect. I also tried fix you suggested for c5760 but it didn't work. Maybe SI-Team can figure that one out.

[mathomp4]

@biljanaorescanin @weiyuan-jiang We need updates to utils_topo/scrip_to_restart_topo.py in this PR to add global attributes if the gwd_internal_rst is for a stretched grid.

The things needed are global attributes like:

		:STRETCH_FACTOR = 2.5f ;
		:TARGET_LAT = 39.5f ;
		:TARGET_LON = -98.35f ;

I want to say you'd do things like:

ncFidOut.STRETCH_FACTOR=2.5
ncFidOut.TARGET_LAT=39.5
ncFidOut.TARGET_LON=-98.35

or something like that? I'm not the best at Python netcdf.

@bena-nasa might know the right thing. But the script needs some way to know if things are stretched.

[biljanaorescanin]

@mathomp4 @bena-nasa I've made changes and tested it will add attributes like this at the end, for example here is from c540 :
// global attributes:
:STRETCH_FACTOR = 2.5 ;
:TARGET_LAT = 39.5 ;
:TARGET_LON = -98.35 ;

and regular grid is same as before I've tried c24. I hope this is what you had in mind.

[mathomp4]

@biljanaorescanin I think you got it!