…timeseries

file to register the maximum values for PCT_NAT_PFT and PCT_CFT through the time series.
This is used to determine how many PFTs and CFTs are instantiated at run time in CLM5

…ut PCT_CROP_MAX in addition to

PCT_NAT_PFT_MAX and PCT_CFT_MAX. This involved modifying the new subroutine to update both p2l and l2g
and renaming it update_max_array. Additional changes were made to match Bill's suggestions of
the sub_routine subname parameter and moving the initial assignment of the max array within the
if (mksrf_fdynuse /= ' ') then code
The code has been tested and produces the maximum PCT_CROP_MAX variable as expected. PJL

…timeseries

file to register the maximum values for PCT_NAT_PFT and PCT_CFT through the time series.
This is used to determine how many PFTs and CFTs are instantiated at run time in CLM5

…ut PCT_CROP_MAX in addition to

PCT_NAT_PFT_MAX and PCT_CFT_MAX. This involved modifying the new subroutine to update both p2l and l2g
and renaming it update_max_array. Additional changes were made to match Bill's suggestions of
the sub_routine subname parameter and moving the initial assignment of the max array within the
if (mksrf_fdynuse /= ' ') then code
The code has been tested and produces the maximum PCT_CROP_MAX variable as expected. PJL

…5_maxpftcft

Begin separating SoilHydrology flux calculations

Note the new tag naming: Starting with this tag, we are naming tags
"ctsm..." rather than "clm...". We are starting with ctsm version 1,
which for now is nearly the same as clm version 5. We are moving to this
new tag naming now because:

(1) The changes in this tag represent the first step towards
    implementing the CTSM vision (separating the biogeophysics flux
    calculations from state updates, making it easier to plug in
    alternative parameterizations, etc.).

(2) This tag changes answers relative to the CLM5 release. (We expect
    the climate to be the same, but we haven't tested this carefully
    yet.)

Purpose of changes
------------------

First steps toward separating various flux calculations in the soil
hydrology code. The focus here is on saturated surface runoff and
infiltration excess runoff. The changes here separate flux calculations
from state updates and extract various calculations into their own
subroutines to facilitate swapping in alternative parameterizations.

Most of the changes here are refactorings that are either bit-for-bit or
just introduce roundoff-level differences. However, there are also a few
larger answer changes, as described below.

These are the greater-than-roundoff-level answer changes:

(A1) Use full qflx_surf in BGC code. Previously, the subroutines ch4 and
     SoilBiogeochemNLeaching had been using a flux that excluded surface
     water runoff (qflx_h2osfc_surf). That was deemed to be incorrect
     (by Dave Lawrence and others), so these BGC subroutines have been
     changed to use the full surface runoff (saturated excess runoff +
     infiltration excess runoff + h2osfc runoff).

     Configurations affected: BGC compsets

     Magnitude of change: Larger than roundoff; expected to be same
     climate, but not investigated carefully

(A2) VIC: Don't ever use the TOPModel formulation for SurfaceRunoff

     The code was using the TOPModel-based formulation for SurfaceRunoff
     if frost_table > zwt_perched. Sean Swenson felt this shouldn't be
     done, and refactoring will be easier if VIC always uses the
     vic-looking formulation, so I'm stopping applying this formulation
     when using VIC.

     Configurations affected: VIC compsets

     Magnitude of change: Larger than roundoff; not investigated carefully

(A3) VIC: Remove infiltration excess runoff

     Martyn Clark reviewed the VIC implementation, and felt that the
     current implementation of infiltration excess runoff is
     inconsistent with the standard VIC implementation. It appears that
     what was being called VIC's infiltration excess runoff was actually
     just an attempt to give a better numerical approximation to the
     solution for saturated surface excess runoff. So deleting this
     leaves only a first-order approximation to VIC's saturated surface
     excess runoff.

     Eventually we may want to put in place a more accurate solution for
     VIC's saturated surface excess runoff. But Martyn's feeling is that
     this can come in with other changes we want to make regarding
     numerical solutions in CTSM.

     Configurations affected: VIC compsets

     Magnitude of change: Larger than roundoff; expected to be same
     climate, but not investigated carefully

(A4) Change in QOVER diagnostic field: now includes QH2OSFC.

These are the major refactorings (either bit-for-bit or just
roundoff-level differences):

(R1) Extract surface runoff to its own module, and other modularization
     related to what used to be subroutine SurfaceRunoff: extract a
     subroutine for each fsat method, move urban surface runoff code
     into different routines.

(R2) Extract infiltration excess runoff to its own module, and other
     modularization related to what used to be subroutine Infiltration.

NOTE: For a detailed breakdown of changes, including documentation of
which changed changed answers, see the file ChangeLog_branch which was
deleted from this branch shortly before it was merged to master.