removed slascaler and various fates parameter changes

[rgknox]

The calculation of leaf biomass was being scaled by the ratio of a parameter slascaler, and slatop. However, this ratio is redundant with the allometric slope parameter. The ratio was removed, and the parameter was removed from the parameter read.

Other wish-list changes to parameters were added to this PR, including: 1) addition of understory collateral damage fraction for logging 2) addition of dbh_repro_threshold, which sets the size where clonal reproduction kicks in, 3) changed max_dbh to allom_dbh_maxheight which is more consistent with the meaning, 4) carbon to biomass multiplier which converts mass in carbon to mass in total biomass.
The dbh_repro_threshold is set equal to allom_dbh_maxheight in the file for now; and while it is read-in, the value is not used until modular allometry is introduced. The understory collateral damage fraction for logging was set to the natural survivorship fraction, again this is read-in but not used.

PR is coupled with fates-clm PR# 27 (https://github.com/NGEET/fates-clm/pull/27 )which updates the default file

Code review:
Test suite: ed.cheyenne.intel , ACRE comparison for 100 year simulation at 4 ngee tropics sites
Base fates Hash: b6b3a86
Base fate-clm hash: 4b4c5a4
Test namelist changes: none
Test answer changes: EXPECTED (part bug fix on bleaf and its derivative, parameters modified to reduce differences)
Test summary: ed.cheyenne.intel: expected PASS, nlcomp and base compares expected FAILS

[rgknox]

Here is the cdl format of the fates parameter file

Here is a diff of the parameter file:

$ diff fates_params_2troppftclones.c171005.cdl fates_params_2troppftclones.c170926.cdl 
1c1
< netcdf fates_params_2troppftclones.c171005 {
---
> netcdf fates_params_2troppftclones.c170926 {
153a154,156
> 	double fates_max_dbh(fates_pft) ;
> 		fates_max_dbh:long_name = "the diameter corresponding to maximum height or stature, diameters may increase beyond this" ;
> 		fates_max_dbh:units = "cm" ;
175,180d177
<         double fates_dbh_repro_threshold(fates_pft) ;
< 		fates_dbh_repro_threshold:long_name = "the diameter (if any) where the plant will start extra clonal allocation to the seed pool (NOT USED YET)" ;
< 		fates_dbh_repro_threshold:units = "cm" ;
< 	double fates_allom_dbh_maxheight(fates_pft) ;
< 	        fates_allom_dbh_maxheight:long_name = "the diameter (if any) corresponding to maximum height, diameters may increase beyond this" ;
< 	        fates_allom_dbh_maxheight:units = "cm" ;
228a226,228
> 	double fates_allom_d2bl_slascaler(fates_pft) ;
> 		fates_allom_d2bl_slascaler:long_name = "allometric SLA_top scalar on bleaf term" ;
> 		fates_allom_d2bl_slascaler:units = "" ;
236,237c236,237
< 		fates_allom_d2ca_coefficient_max:long_name = "max (savanna) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ;
< 		fates_allom_d2ca_coefficient_max:units = "m2 cm^(-1/beta)" ;
---
> 		fates_allom_d2ca_coefficient_max:long_name = "max (savanna) dbh to area multiplier factor where: area = pi*n*d2ca_coeff*dbh^beta" ;
> 		fates_allom_d2ca_coefficient_max:units = "m2/cm" ;
239,240c239,240
< 		fates_allom_d2ca_coefficient_min:long_name = "min (forest) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ;
< 		fates_allom_d2ca_coefficient_min:units = "m2 cm^(-1/beta)" ;
---
> 		fates_allom_d2ca_coefficient_min:long_name = "min (forest) dbh to area multiplier factor where: area = pi*n*d2ca_coeff*dbh^beta" ;
> 		fates_allom_d2ca_coefficient_min:units = "m2/cm" ;
488c488
< 		fates_logging_collateral_frac:long_name = "Fraction of large stems in upperstory that die from logging collateral damage" ;
---
> 		fates_logging_collateral_frac:long_name = "Fraction of stems killed due to collateral damage per event" ;
490,492d489
< 	double fates_logging_coll_under_frac(fates_scalar) ;
< 		fates_logging_coll_under_frac:long_name = "Fraction of stems killed in the understory when logging generates disturbance" ;
< 		fates_logging_coll_under_frac:units = "fraction" ;
497,498c494
< 		fates_logging_event_code:long_name = "Integer code that options how logging events are structured" ;
< 		fates_logging_event_code:code_meanings = "see biogeochem/EDLoggingMortality.F90:IsItLoggingTime() for logic" ;
---
> 		fates_logging_event_code:long_name = "Integer code that options how logging events are structured (NOT USED)" ;
620,622c616
<  fates_allom_dbh_maxheight = 150, 150 ;
< 
<  fates_dbh_repro_threshold = 150, 150 ;
---
>  fates_max_dbh = 150, 150 ;
664c658
<  fates_allom_d2bl1 = 0.07, 0.07 ;
---
>  fates_allom_d2bl1 = 0.028, 0.028 ;
669a664,665
>  fates_allom_d2bl_slascaler = 0.03, 0.03 ;
> 
674c670
<  fates_allom_d2ca_coefficient_max = 0.656846381604825, 0.656846381604825 ;
---
>  fates_allom_d2ca_coefficient_max = 0.3, 0.3 ;
676c672
<  fates_allom_d2ca_coefficient_min = 0.338111885296947, 0.338111885296947 ;
---
>  fates_allom_d2ca_coefficient_min = 0.18, 0.18 ;
784c780
<  fates_fdi_a = 17.62 ;
---
>  fates_fdi_a = 17.27 ;
786c782
<  fates_fdi_b = 243.12 ;
---
>  fates_fdi_b = 237.7 ;
880,881d875
<  fates_logging_coll_under_frac = 0.55983 ;
< 
884c878
<  fates_logging_event_code = -30 ;
---
>  fates_logging_event_code = 1 ;

[ckoven]

Looks great to me. Thanks @rgknox