bug-fixes to impact mortality, litter and line-lengths

Changes in this release since sci1.4.0_api.3.0.0 are almost exclusively bug fixes. Work done by C. Koven and E Kluzek, targetting fixes to impact mortality and litter accounting bug-fixes, line-length fixes respectively.

logging, prescribed-phys, C-balance fixes, spread logic, thread-fix, parameters

This tag contains several science updates, bug fixes and API changes.
The logging module was introduced
A namelist parameter use_logging is expected from the host land model*
A prescribed physiology mode was introduced, NPP is prescribed and photosynthesis/respiration is ignored
Bug fixes were applied to carbon accounting and calculation of leaf biomass
Modifications were made to the calculation of canopy spread, shifting it to the site level
Various updates to parameters, names, values and metadata, see fates_params_2troppftclones.c171010

This tag is compatible with fates-clm clm4_5_15_r234_v1.1.0_fatesAPI_v3.0.0
*This tag is NOT backwards compatible with clm4_5_15_r234_v1.1.0_fatesAPI_v2.0.0

bug-fix on canopy understory demotion, added NCARs flat-history

This release contains a bug-fix on canopy understory demotion.

Updated parameter and namelist interface

This is a backwards incompatible tag that is only compatible with fates-clm major release API 2. Updates were made to how fates allocates pft space, and ingests parameters and namelist entries. Also some cleaning was performed on the history dimensions part of the interface.

Partial Non-Disturbance Generating Canopy Mortality

A feature was added in this release where mortality in the canopy will only generate disturbance at a fraction of 100% of the total potential rate.

New history diagnostics, increment variable bugfixes, burned area updates

As stated in the name, this release features new history diagnostics, updates to the burned area calculations in the spit-fire model and bug-fixes. The bug fixes include the addition of various state variables including growth increment to cohort copy and fusion functions. The burn area may be considered a fix. Syntactical improvements were also made, including the nesting of logging statements behind debug calls.

Added inventory initialization (no api changes)

This release added inventory initialization. The file and switching of this function on and off are hard coded and does not update the API at all.