CLM Urban Model Work to checkin to Trunk (clm3_5_16)

clm3_expa_54 - finemesh updates - bfb with expa_48
clm3_expa_66 - Tony restructuring, share clocks, various updates - bfb except in CN mode and for time-manager
clm3_expa_79 - misc changes, memory restructuring - bfb (except RTM)
clm3_expa_87 - new configure tests - changes answers - new Hydro
clm3_expa_99 - Move externals to top - changes answers - BTRAN, others
clm3_5_09 ----- Latest clm version - changes answers, surf-datasets
clm3_5_15 ----- Tag before checkin of Urban to trunk.
clm3_5_16 ----- Urban tag.
Task list:

List of tasks once science branch is on trunk

Modify so that urban columns can work with 15 layers (default for new CLM) - DONE
How to handle urban heat source
Fix indexing bug in SoilTemperature related to SNICAR in clm3_6_15 - DONE
Fix rootfr_road_perv setup (change from 1,nlevgrnd to 1,nlevsoi and 0 elsewhere) - DONE
Change urban soil properties in iniTimeConst.F90 to use CLM4 equations (w/organic soil) but with organic soil set to zero. - DONE
Urban does not have SNICAR snow in it. OK? OK! - DONE
Commit mksrfdat code related to replacing bare soil preferentially with urban.
Decide on 0.1% or 1% threshold. Either way, generate new surface dataset and associated parameter file because current default dataset uses 1% threshold but does not preferentially replace bare soil with urban.
Check proper averaging of fields being passed to atmospheric model (again)
Add namelist options for 1) no URBAN_AC/_HEAT OR URBAN_AC/_HEAT, 2) no WASTEHEAT or WASTEHEAT - DONE
Change AC and HEAT efficiencies (15-30% and 80%)? 25% AC, 75% HEAT - DONE
Review all history fields for proper averaging (including those for CASA, DUST, etc.)
Set set_nourb=0 for history fields WASTEHEAT, BUILDHEAT, URBAN_AC, URBAN_HEAT, TRAFFICFLUX, Qanth - DONE
Fix water balance error due to snow capping in urban - DONE
Datasets - set up proper averaging of urban parameters and urban fraction to desired resolutions and put everything into netcdf.

Checkin last changes into CVS - DONE
Verify scripts and testing scripts on this version - DONE
Update branch from clm3_expa_41 to clm3_expa_48 - verify works correctly - DONE
Move branch from CVS to SVN - DONE
Examine differences between Urban model and clm3_expa_48. - DONE
Update to clm3_expa_54 DONE
Update to clm3_expa_66 DONE
Update to clm3_expa_79 DONE
Update to clm3_expa_87 DONE (Keith Validated, no-pervious is identical to _54)
Update to clm3_expa_99 DONE (Keith Validated, TKFRZ only change)
Testing clm3_expa_99 on other platforms (DONE)
Update to clm3_5_09 (DONE) (Keith Validated)
Update urban scripts, add in datasets, add urban tests to test_driver.sh (DONE)
Update to clm3_5_15 (DONE)
Move tests in testurban.csh script to test-driver.sh DONE
Remove URBAN_TESTING, URBAN_OUTPUT, URBAN_LONGW, URBAN_FORCT DONE
Make URBAN_SOLAR the default, check what datm7 does
Verify and validate new Urban model branch (Keith) (DONE)
Changes required to check into clm_dev
Make sure urban datasets are in XML file. DONE
Make sure unneeded CPP options are removed. DONE
Add new Urban tests into configure, build-namelist and test suite DONE