Added the following new input forcing variables (used for simulations
of carbon cycle processes):
  CATM: Atmospheric CO2 mixing ratio [ppm]
  FDIR: Fraction of incoming shortwave that is direct [fraction]
  PAR:  Photosynthetically active radiation [W/m2]

These variables are optional; if not supplied as forcings, VIC will use
default values for them, as follows:
  CATM: Value of CatmCurrent defined in vicNl_def.h
  FDIR: Value computed by MTCLIM module
  PAR:  SHORTWAVE*SW2PAR, with SW2PAR defined in vicNl_def.h

Similarly, added the following new output variables:
  OUT_CATM:   (equals CATM)
  OUT_COSZEN: Cosine of the solar zenith angle, computed by MTCLIM module
  OUT_FDIR:   (equals FDIR)
  OUT_PAR:    (equals PAR)
Added simulation of photosynthesis.  The photosynthesis formulation was
taken from the BETHY model (Knorr, 2000), which in turn used the Farquhar
model for C3 plants and the Collatz model for C4 plants.  In addition,
inhibition of photosynthesis under saturated conditions (as described
by Frolking et al, 2002) is allowed for.

This feature requires several new veg parameters to be in the veg
library file:
  Ctype:          Photosynthetic pathway; can be C3 or C4
  MaxCarboxRate:  Maximum carboxlyation rate at 25 deg C (mol(CO2)/m2s)
  MaxETransport:  Maximum electron transport rate at 25 deg C (mol(CO2)/m2s) (C3 plants)
  CO2Specificity: CO2 specificity at 25 deg C (mol(CO2)/m2s) (C4 plants)
  LightUseEff:    Light-use efficiency (mol(CO2)/mol(photons))
  NscaleFlag:     TRUE = nitrogen-scaling factors are applicable to this veg class
  Wnpp_inhib:     Moisture level (fraction of maximum moisture) above which photosynthesis experiencing saturation inhibition, i.e. too wet for optimal photosynthesis; only applies to top soil layer
  NPPfactor_sat:  Photosynthesis multiplier (fraction of maximum) when top soil layer is saturated

There are several new output variables associated with this feature:
  OUT_GPP:  Gross primary productivity [g C/m2d]
  OUT_RAUT: Autotrophic respiration [g C/m2d]
  OUT_NPP:  Net primary productivity [g C/m2d]
  OUT_APAR: Absorbed PAR [W/m2]

By default, this feature is turned off.  To turn this feature on, set
CARBON to TRUE in the global parameter file.

When this feature is turned on, you can choose to compute stomatal
resistance via the Jarvis formulation (the formulation used by all
previous versions of VIC) or as a function of photosynthetic demand.
This is determined by the setting of RC_MODE in the global parameter
file.  A value of RC_JARVIS (which is the default) selects the Jarvis
formulation.  A value of RC_PHOTO selects the photosynthetic demand
formulation.
Fixed if statement surrounding calc_rc call to include check on options.CARBON.
Previous commit contained incomplete fix.
Added another if statement regarding options.CARBON.
Fixed yet another bug.
Fixed yet another missing check on options.CARBON.
Added simulation of soil carbon storage and fluxes.  This formulation was
taken mostly from the LPJ model (Sitch, 2003), which in turn used a
Lloyd-Taylor model for the dependence of soil respiration on soil
temperature.  The dependence of soil respiration on soil moisture was
based on the formulation of Yi et al (2012) but modified to allow a small
respiration rate under saturated conditions.

At this point, we do not simulate the storage of carbon in living biomass.
Therefore, the flux of carbon into the soil (litterfall) is set equal to
the total NPP of the previous calendar year, spread evenly over the current
year.  As in the LPJ model, soil carbon is stored in 3 pools: litter (fast),
intermediate, and slow; with associated turnover times of 2.86 y, 33.3 y, and
1,000 y, respectively.  Litterfall enters the litter pool.  Carbon exits the
litter pool through respiration (RhLitter).  A fraction (fAir) of this
respired carbon is in the form of CO2 and is vented directly to the atmosphere
(RhLitter2Atm).  The remainder is sent to the intermediate and slow pools
in the proportions fInter and (1-fInter), respectively.  These pools also
respire carbon, which is assumed to be in the form of CO2 and vented directly
to the atmosphere.

There are several new output variables associated with this feature:
  OUT_RHET: Total heterotrophic respiration vented to the atmosphere
            (= RhLitter2Atm+RhInter+RhSlow)  [g C/m2d]
  OUT_NEE:  Net Ecosystem Exchange (= NPP-RHET) [g C/m2d]
  OUT_LITTERFALL: Flux of carbon from living biomass into litter pool [g C/m2d]
  OUT_CLITTER: Carbon density in the litter pool [g C/m2]
  OUT_CINTER: Carbon density in the intermediate pool [g C/m2]
  OUT_CSLOW: Carbon density in the slow pool [g C/m2]

This feature is part of the carbon cycle, controlled by the setting of the
CARBON option in the global parameter file.
Added soil moisture content for half-space below bottom soil layer.

VIC's soil thermal profile can extend well below its soil hydrologic
layers.  Previously, the moisture content of these soil thermal nodes
was set to that of the bottom soil layer.  Now, the moisture content can
be set to a user-specified value, SLAB_MOIST_FRACT, defined in
vicNl_def.h.
Implemented heat flux between lake and underlying soil.

Previously, the lake bottom was treated as a no flux boundary, so
that no heat traveled between the lake and the underlying soil.  Soil
temperatures in the lake/wetland tile were determined only from the
energy fluxes through the wetland surface.  In other words, the soil
under the lake had the exact same temperature as the soil in the
exposed wetland, as if the lake were not present.

Now, the soil under the lake has its own temperature profile,
independent of that in the exposed wetland.  Heat and any un-absorbed
shortwave radiation in the lowest lake layer now can pass into the top
of the soil column beneath the lake.

There are now two new output variableis that track the soil temperature
profile under the lake:
  OUT_SOIL_TEMP_LAKE:  Average temperature in the hydrologic soil layers beneath the lake
  OUT_SOIL_TNODE_LAKE: Soil thermal node temperatures beneath the lake
reverted Ted's branch to commit before dist. water table
Merge branch 'feature/VIC_4.1.2.wetcarb.new' into develop

Conflicts:
	src/initialize_model_state.c
Merge pull request #44 from jhamman/feature/VIC_4.1.2.wetcarb.new

Merge Feature/vic 4.1.2.wetcarb.new into development branch