updates to the parameter file

[rgknox]

Description:

The default parameter file has been expanded to accomodate 13 PFTs, including temperate, boreal, evergreens, stress deciduous, cold deciduous, shrubs and grasses. These PFTs are not optimized, nor have they experienced any parameter sensitivity evaluation. Many parameter were derived from earlier estimates provided by @jenniferholm, but have since been slightly modified, and there should be no expectations from other users that they will generate usable or scientifically valid results.

The current purpose of the default parameter file is only to check that as many functions and procedures in the model software are exposed to stress testing.

New parameters added: logging_dbhmax_infra (including procedures to read in), clumping_index (including procedures to read-in), maintresp_reduction_curvature and maintresp_reduction_intercept.

Parameter re-named: clone_alloc has changed to seed_alloc_mature.

The "CDL" or text version of the default is now being updated in the file: parameter_files/fates_params_default.cdl

A new subroutine was added that does checks on input parameters, such as checking maximum allowable ranges, or simple logic tests (e.g. a plant cant be deciduous and evergreen at same time..)

fates_allom_stmode is now reading in the actual values from the file, and is no longer a dummy parameter

fates_branch_turnover is now reading in the actual values from the file, and is no longer a dummy parameter

Corresponds with clm-fates PR 33, https://github.com/NGEET/fates-clm/pull/33

WILL INCREMENT API TAG TO 3.1.0

Collaborators:

See thread: #337, @huangmy , @xuchongang , @jkshuman , @jenniferholm , @ckoven , @serbinsh , @mpaiao , @rosiealice

Expectation of Answer Changes:

Oh yes... this will certainly change answers, the plants are all different.

Checklist:

• My change requires a change to the documentation.
• I have updated the in-code documentation AND wiki accordingly.
• I have read the CONTRIBUTING document.
• FATES PASS/FAIL regression tests were run
• If answers were expected to change, evaluation was performed and provided

Test Results:

Tests run on lawrencium and cheyenne, reverted to FATES-CLM as driver because of issues in testing system with CTSM (MPT errors, could be time-outs with longer run times...)

FATES-CLM hash: aa1c48c

All expected PASS.

Expected FAILS:

 FAIL ERP_Ld9.f45_f45.ICLM45ED.cheyenne_intel.clm-FatesAllVars COMPARE_base_rest
  FAIL ERS_Ld60.f45_f45.ICLM45ED.cheyenne_intel.clm-FatesFinif45 COMPARE_base_rest
  FAIL ERS_Ld60.f45_f45.ICLM45ED.cheyenne_intel.clm-FatesLogging COMPARE_base_rest
  FAIL ERS_Ld60.f45_f45.ICLM45ED.cheyenne_intel.clm-FatesPPhys COMPARE_base_rest
  FAIL ERS_Ld60.f45_f45.ICLM45ED.cheyenne_intel.clm-FatesST3 COMPARE_base_rest

[rgknox]

Deciduous trees are currently breaking carbon balance checks. The failures are not immediate, but seem to kick in after a year with the new parameter set after 1 1/2 years on the f45 grid.

I'm running some new tests now, first to see if setting all 13 pfts to evergreens will run indefinitely while passing carbon balance checks.

Depending on how obscure the carbon balance bug is, I may temporarily set all trees to evergreen to get this PR through, as various other updates to the parameter file are holding other PRs up.

[rgknox]

Added entry for height structured variables per #355
Forcing all 14 PFTs to be evergreens until carbon balance issues are solved. See issue #356.

[rgknox]

Several more rounds of testing and updates have been added to this PR.

Some warnings during canopy area profiling, were just recently changed to fails, but those fails are now triggering with the new demography. I added a debug flag and/or removed the checks as they were not the correct location anyway, and this is a different issue.

The indexing of C3/C4 flags during photosynthesis, as pointed out by @huitang-earth, have been fixed

Integrated naming convention updates and default file organization by @ckoven

Testing on cheyenne now