…quires other subroutines to the list as well as some additional functons to mkncdio.F90

… also add the unit test build to the git ignore

…umpft outside of if, and handle case when all PFTs are set

…arlier mkpftMod.F90 version

…nd pft override)

…ero-out and pft unit tests, also zero-out doesn't need to read in datasets in mkpft and tgridmap doesn't need to be cleaned at the end of mkpft for these two cases

…ween the two

…CFTs

… oldformat is flagged

…rom both zeroout and index provided methods

…for the zero out option

… start using stored indices for some values

…f true

…special case of use_input_pft, make all_veg a local input to mkpftInit and create a global one that is set in mkpftInit, also add it to the namelist

Remove global all_veg and add in presc_cover in it's place. all_veg
now comes as input to mkpftInit and helps set presc_cover. Unit
tests updated and working.

…ll be set for prescribed PFT cases that use dataset PCT_NAT_VEG and PCT_CROP

… can run with threading on fixing ESCOMP#791

…ded to the front of them

…esfor5028

…is decommisioned

…control fndep file, continue to use the historical fndep file so that answers don't change

This reverts commit 43529b6:

Revert the change in urbantv for clm4_5 as it changes answers in
some cases.

… seperate part of driver can be called from. Also add some SHR_ASSERT calls for checking it, add a new diagonstic history variable for H2OSOI as read from streams so can compare to input, make the calls to new subroutine in the original place which shouldn't change answers, but it does unexpectedly

Properly send $opts down to it, and use it in calls inside.
Also add a check that this isn't a transient use case for soil
streams with linear time-interpolation as that will likely cause
an error going from a vegetated point that is missing to not, or
vice versa. Also add a check for that. And fix the soilm test which
had phys in place of conopts.

Change h2osoi_prs to be on gridcell. Do some checking for spval
in soil moisture streams. Added a check that prints a warning
and a commented out endrun (until we have a dataset in full agreement).

…esfor5028

Add new namelist item soilm_ignore_data_if_missing and react to it.
Also use old way for the indexing in an attempt to reproduce the
previous results. If soilm_ignore_data_if_missing is true and find
a missing point expected continue calculation as before. If not
abort when that point is found. Also comment out the section
where values greater than 10 were set to spval as that changes
answers.

OK, this is a version that is identical to release-clm5.0.27. Found out
the issue was that lai_interp can't be moved the way I did. It needs
to be divided into the streams part and non-streams part like is
being done in SoilMoistureStreams.

So this replicates answers for SMS_P720x1_D_Ld3.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-prescribed

… level and SoilMoistureInterp to the OMP clump level

…nd lai_interp called from within an OpenMP threading loop

…t case

Add tintalgo settings for most of the streams. Also
change the buildnml fatal-error for soilm_tintalgo='linear'
for transient to a warning that can be overridden if desired.
Also fix the build-namelist unit test for warnings, so it
verifies that warnings die, but will run if -ignore_warnings
is set. Also get maxpatch_pft to normally die if the two
valid settings are used (79 or 17).

…or soil moisture streams)

…me that gets them to work)

…esfor5028