This is part of the labels / documentation for <a href='http://jcm.chooseclimate.org'>Java Climate Model</a><hr/>

#carboncycle		¨oldJCM4 addJCM5		§This  is a linker module, an interface between the @berncarbon and the rest of JCM, taking emissions from  @globco2emit and passing the concentration onto @radfor. 

This separation of the input/output from the detail of the calculation makes it possible to substitute the @berncarbon for another model (such as the simple  @accccarbon which is embedded within this module).

It also contains the @qtsets for atmospheric CO2 concentration and fluxes. 
The change in atmospheric CO2 concentration is the sum of fossil and land-use emissions, minus the ocean and biosphere sinks, which  respond dynamically to concentration and temperature (see @berncarbon for details).

Note also some related @qtsets {{ 
*: @carbonstoragecurves 
*: @co2equivconc 
}} and further information in {{
*: @sinksdynamic, *:@sinksocean, *:@sinksbiosphere, *:@carbchem
}}
</ul>

#atco2plot		¨oldJCM4		§£>atco2conc

#totemit		¨oldJCM4		§Sum of @fossilemit and @lucemit
When this equals @totsink the @atincmod will be zero

#fossilemit		¨oldJCM4		§Begins with @history, continues into the future with @stabilisation scenarios (or @aboutsres if the @objective is no-policy)

#lucemit		¨oldJCM4		§History from @CalcLucEmit ,  future  from  @globco2emit (combining @aboutsres and  @stabilisation -note, some senarios have negative LUCF emissions, implying net regrowth / sequestration).

#totsink		¨oldJCM4		§Sum of @oceansink and @landsink 
When this equals @totemit, @atincmod will be zero

#oceansink		¨oldJCM4		§Net flux into the ocean
Calculated by @berncarbon, see also @sinksocean
(a plot of @carbonstoragecurves shows more detail)

#landsink		¨oldJCM4		§Net sum of increased photosynthesis due to carbon fertilisation, and increased soil respiration due to rising temperatures.
Calculated by @berncarbon, see also @sinksbiosphere
(a plot of @carbonstoragecurves shows more detail)

#atco2data		¨oldJCM4		§For comparison with the calculated curve

#atco2calc		¨oldJCM4		§The concentration calculated by the model.
The change in concentration is simply the sum of the emissions, minus the sinks (adjusting units to take into account the volume of the atmosphere). 
It is useful to consider this together with a plot of @atco2flux : The concentration rises when @totemit (brown) curve is above @totsink (cyan), or vice versa.

#atco2		¨oldJCM4 addJCM5		§Regional Contributions to Atmospheric CO2

(in ppm, right hand scale)

#hdmbopt		¨oldJCM4		§Calculate LUCF emissions required to reach measured CO2 concentration

#lucfemit1990		¨oldJCM4		§Scales all historical LUCF emissions (dataset from Houghton et al)

#carbonstoreplot		¨oldJCM4		§£^apptag This plot shows the contents of all the boxes in the carbon cycle model (ocean layers and biosphere). The curves are simply the contents of the cq array in the @carboncycle . These contain only "extra" anthropogenic carbon, excluding the contents in the preindustrial steady state. See also @atco2plot.
  %% ¤adju Note: It is easier to understand the effect of the @carboncycle parameters, when the model is working in forwards rather than @inverse mode: -see @sinksdynamic%%
  £§graphinfo ££sinksbiosphere ££sinksocean ££carbchem

#fertbeta		¨oldJCM4		§(see @sinksbiosphere)

#resp_q10		¨oldJCM4		§(see @sinksbiosphere)

#cupwell		¨oldJCM4		§(see @sinksocean)

#chighlat		¨oldJCM4		§(see @sinksocean)

#csidemix		¨oldJCM4		§(see @sinksocean)

#ceddydiff		¨oldJCM4		§(see @sinksocean)

#asgasex		¨oldJCM4		§see @sinksocean for more info
(included within @carbonatechemistry for convenience of model structure).
This  parameter doesn't make much difference to the model, unless you reduce it to almost zero, because air-sea exchange is not usually the rate-limiting process. However it's value is important for quantifying the current carbon budget from measurements.

#chemfbopt		¨oldJCM4		§see @carbonatechemistry and @clicarbfeedback for more info

#carbchemmenu		¨oldJCM4		§see @carbonatechemistry for more info

#realb		¨oldJCM4		§Real Chemistry inc Borate (Ben iteration method) -see @carbchem

#realj		¨oldJCM4		§Real Chemistry inc Borate (Jesper iteration method) -see @carbchem

#hildaz0z1		¨oldJCM4		§z0z1 Method used in original Hilda model  -see @carbchem

#cubicfit		¨oldJCM4		§Better than Linear, but not so good as Real chemistry (note: Hilda options does better for low emissions scenarios, and this one for high emissions scenarios)

#linear		¨oldJCM4		§Many simple models assumed a linear response. However you can see that this significantly overestimates the ocean sink, compared to the formulae including the chemistry feedback. -see @carbchem

#carbonemissions		¨oldJCM4 addJCM5		§£>globco2emit

#carbonmodel		¨oldJCM4		§The carbon cycle is based on the Bern model, as used by IPCC. This was originally calibrated using chemical tracer and isotope data, and its predictions fall in the mid-range of model intercomparisons.
  ---- ===Ocean sink: HILDA model ===
  (HILDA = High-Latitude Diffusion Advection)   <li>low-latitude (84% surface) divided into 36 layers   <li>depth-dependent vertical diffusion between layers   <li>high-latitude box, well-mixed   <li>horizontal advection between HL & LL   <li>slow upwelling loop (down in HL, up in LL)   <li>surface layer (HL and LL) exchanging with atmosphere   <li>non-linear carbonate chemistry with feedback from temperature
  ---- ===Terrestrial Biosphere sink===
  4-box biosphere :   <li>green, wood, soil, humus boxes,   <li>linear fluxes between boxes and to atmosphere   <li>non-linear "CO2 fertilisation" factor 'beta'   <li>(note further development below)
  ---- ===Calculation method===
  The entire system is solved using an efficient eigenvector calculation method with a ramp function for non-linear fluxes.
  <hr> See also<li> Joos et al 2001 (@references),<li>@eigenvec,<li>@compareipcc, IPCC-TAR WG1 Chapter 3

#carbonfuture		¨fut		§{{
<li>The simple 4-box biosphere is based on Bern model as used in IPCC-SAR. The Bern-CC biosphere as used for IPCC-TAR includes a more complex gridded dynamic vegetation model with many plant functional types, dependent on temperature an precipitation within each gridcell.  A java implementation of this was under development, and may be resumed.  <li>There is not yet any biology in the ocean sink model. The original assumption was that the "biological pump" is not climate or CO2 dependent, on the other hand it may be affected by circulation changes affecting nutrients, the range of this uncertainty should be illustrated. 
}}

#sinksdynamic		¨oldJCM4		§Both sinks increase in response to rising atmospheric CO2.
  It is easier to understand see this effect in a "forward" calculation, applying the "£~nopolicy" or the "£~stabemit" option (see @objective, @stabilisation). Then, if you increase one of the sinks by adjusting the model parameters, the atmospheric CO2 falls slightly, and so the other sink drops. However, when you run the model in inverse mode, adjusting the sink parameters will cause the emissions to change, in order to continue to reach the target concentration or temperature curve (see also @inverse)%%.

#sinksbiosphere		¨oldJCM4		§The green/brown curves in @carbonstoragecurves show the amount of extra (anthropogenic) carbon taken up by the terrestrial biosphere (green plants, wood and soil) due to the "CO2 fertilisation" effect (photosynthetic carbon fixation is slightly more efficient at higher CO2 concentrations). You can adjust with with the @fertbeta parameter.
  Later, the biosphere sink begins to "saturate", as other factors such as water, sunlight and nutrients become more rate-limiting than CO2 for photosynthesis.
 A simple temperature-respiration feedback has also been added, using a formula similar to that developed by Cox et al. You can adjust the 'q10' factor using the @resp_q10 control. The effect is to reduce the storage of carbon in the soil, especially in later years when temperatures are higher.

Note also  @clicarbfeedback, @carbonfuture

#sinksocean		¨oldJCM4		§The ocean has a very large capacity to store CO2 (due to chemical buffering - see below). However the mixing between surface water and deep water is very slow, so the uptake of anthropogenic CO2 is dependent on the mixing rate. This mixing is dominated by the vertical diffusion and horizontal advection.  The @ceddydiff parameter controls the rate at which CO2 mixes vertically in the bulk of the ocean.

¤adju  If you select "expert" from the @complexity menu, you can see more parameters, and compare the relative importance of processes. The upwelling loop makes only a small difference. The effect of the gas-exchange rate is also small (unless you cut it altogether), since the mixed surface layer quickly catches up with the atmosphere.

  Note that the upwelling is more important in the heat-flux UDEB model (see @udebclimod) which has no horizontal advection. There is some physical sense in this difference structure, since mixing depends on density gradients which depend on temperature, so this effect supresses mixing of heat in a way that does not affect CO2.

#carbchem		¨oldJCM4		§£§carbonatechemistry

#co2rf		§See @radforco2