Add EQ to evaluate potential for crown fire
Add EQ for passive crown fire igntion
Set fraction of crown burnt based on this conditional
Add crown fire threshold, crown fire flag, and crown fire PFT param

Following @jkshuman's introduction of the Bessie and Johnson (1995)
formulation for determining the presence of passive crown fire
(NGEET#572),
I now add the same paper's formulation for determining the presence of
active crown fire.

The corresponding issue is NGEET#573

Co-Authored-By: Samuel Levis <[email protected]>

…active_crown_fire

Resolved conflicts in
 	fire/SFMainMod.F90

…active_crown_fire

Resolved Conflicts:
 	main/EDTypesMod.F90

Also made two crown-related history varialbes active

…crown_fire

Co-Authored-By: Samuel Levis <[email protected]>

…active_crown_fire

Resolved conflicts in:
 	fire/SFMainMod.F90
 	main/EDTypesMod.F90

This pft-dependent parameter is set in the fates params file.
Use it instead of setting fraction_crown_burned = 1 for all passive
crown fires.

Co-Authored-By: Samuel Levis <[email protected]>

Co-Authored-By: Samuel Levis <[email protected]>

…active_crown_fire

Hoping that this returns to normal fire behavior. Problems reported
previously:
- @slevisconsulting saw fire in year 1 and not after
- @jkshuman saw fire in years 1-5 and not after

The two new flags identifying when passive and active crown fires
occur needed to be integers for the if statements to work correctly.

To facilitate my debugging, I reverted some aesthetic code mods to look
more like @jkshuman's read_lightning_pr561 branch
(https://github.com/jkshuman/fates/tree/read_lightning_pr561) so as to
minimize unnecessary diffs when typing "git diff read_lightning_pr561".
These mods will likely make it back into this branch (active_crown_fire)
with later updates.

I.e. currentCohort%n and currentCohort%c_area.
Also
1) Moving active crown fire calculations inside the if statement that
   confirms ignition of a passive crown fire to increase code efficiency
2) Introducing diagnostic write statements to investigate crown fire
   behavior; remove in a later commit.

Previous commits computed the occurrence of active crown fire and set
currentCohort%fraction_crown_burned = 1.0_r8

Here I begin to introduce the effects of active crown fire on the size
and intensity of the fire as discussed with @jkshuman in NGEET#573. First
step in this is the effect of active crown fire on the Rate of Spread.

I have confirmed that, with the code changes this far,
history varialbes FIRE_ROS, SUM_FUEL, fire_fuel_bulkd have changed,
while fire size and intensity have not changed. This is what I expected.

1) Moved calculation of currentPatch%sum_fuel out of
subr. rate_of_spread and into subr. characteristics_of_fuel because
rate_of_spread is called twice now, yet currentPatch%sum_fuel
should not be updated a second time.
2) Set currentCohort%active_crown_fire_flg back to 0 after the
second call to rate_of_spread because we want it equal to 0 when we
make the next timestep's first call to rate_of_spread.

In the most recent commits I added a second call to rate_of_spread.
After that call I now also call the following subroutines a second time:
- fire_intensity
- area_burnt
- crown_scorching
- crown_damage

In the last commit I initialized currentCohort%active_crown_fire_flg
in an awkward location. I have moved to subr. fire_model where other
variables are initialized.

…active_crown_fire

Resolved Conflicts:
 	biogeochem/EDCohortDynamicsMod.F90
 	fire/SFMainMod.F90

Resolved conflicts:
fire/SFMainMod.F90
main/EDPftvarcon.F90
main/EDTypesMod.F90
main/FatesInterfaceMod.F90
parameter_files/fates_params_default.cdl

This and next few commits resolve conflicts missed by git and caught by
github

Committing only to get ./manage_externals/checkout_externals to finish

Using existing test:
SMS_Lm12_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesFireLightningPopDens

There were two copies of this parameter: a scalar and an array and the
model was getting confused when trying to read them

I found references to both currentCohort%active_crown_fire_flg and
currentPatch%active_crown_fire_flg and I think the latter is correct
and the former incorrect

Calculate required intensity to scorch crown and canopy, then re-calculate
rate of spread and fire intensity

Fixes: 573

User interface changes?: No

Code review:

Fix mistake in equation to solve for phi_wind as part of steps towards calculation of canopy fraction burnt.