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

#carboncycle		§This module calculates the change in atmospheric CO2 concentration, which is the sum of fossil and land-use emissions, minus ocean and biosphere sinks. The sinks respond dynamically to concentration and temperature.
  <hr>See also @atco2plot, @carbonstoreplot , @sinksdynamic, @sinksocean, @sinksbiosphere, @carbchem
  £§iobinfo ££carbonemissions ££carbonmodel  ££carbonfuture

#atco2plot		§£^apptag This plot shows how emissions and sinks of CO2 affect the concentration of CO2 in the atmosphere.   <li>² @carbonstoreplot shows more detail of where the carbon goes when it leaves the atmosphere, and contains controls for adjusting sink uncertainties. ²  <li>² By default (changed with @emitmenu) JCM will stabilise CO2 concentration - see @stabconcdoc, @stabilisation ²
  £§graphinfo ££sinksdynamic
  <hr>The calculations are made in @carboncycle using @carbonmodel. See also   <li>@sinksbiosphere,<li>@sinksocean,<li>@carbchem,<li>@carbonstoreplot  <li>²°adju If expert is selected from @complexitymenu, you can also see curves for @co2eq ²

#totemit		§Derived from either @mitigation or @sres

#fossilemit		§Same as total in @distribplot, but the timescale here is longer

#lucemit		§For SRES scenarios, this comes from @aboutsres (note, some scenarios have negative LUCF emissions, implying net regrowth / sequestration). For Mitigation scenarios, land-use is simply a constant fraction of the total.

#totsink		§Sink curves show the net flux <i>out</i> of the atmosphere (see @carbonstoreplot for detail of sinks and carbon cycle parameters)

#oceansink		§Includes deep ocean mixing, and carbonate chemistry feedback.

#landsink		§Includes 'CO2 fertilisation' of terrestrial biosphere

#atco2data		§For comparison with the calculated curve

#atco2calc		§(concentration in ppm, right hand scale) The change in concentration is simply the sum of the emissions, minus the sinks. So, concentration rises when the brown curve is above the cyan curve, or vice versa.

#atco2		§(in ppm, right hand scale)

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

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

#carbonstoreplot		§£^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.
  ² °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 @sinksdynamic²
  £§graphinfo ££sinksbiosphere ££sinksocean ££carbchem

#fertbeta		§(see @sinksbiosphere)

#resp_q10		§(see @sinksbiosphere)

#cupwell		§(see @sinksocean)

#chighlat		§(see @sinksocean)

#csidemix		§(see @sinksocean)

#ceddydiff		§(see @sinksocean)

#asgasex		§(see @sinksocean)

#chemfbopt		§(see @carbchem, @flowchart)

#carbchemmenu		§see @carbchem

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

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

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

#cubicfit		§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		§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		§Historical fossil CO2 emissions are from CDIAC (add ref!) and land use change CO2 emissions data is from Houghton et al (add ref!), (unless you select the option to calculate historical land-use by mass-balance, fixing the atmospheric CO2 using the measured data from Mauna Loa).
  Future emissions are determined either by @mitigation module (applying a fixed fossil : landuse ratio) or by @sres module.

#carbonmodel		§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.
  ³Ocean sink: HILDA model ³
  (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
  ³Terrestrial Biosphere sink³
  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)
  ³Calculation method³
  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.  <li>Note also @scalelanduse

#sinksdynamic		§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 (@emitmenu). 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)².

#sinksbiosphere		§The green/brown curves shows 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 control.
  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.

#sinksocean		§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 (blue arrow) controls the rate at which CO2 mixes vertically in the bulk of the ocean.

  If you select "expert" from the @complexitymenu, you can see more controls, and can 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 @heatflux) 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		§CO2 reacts with alkaline seawater to form bicarbonate ions
  CO2 + H2O <=> HCO3- + H+
  This conversion reduces the partial pressure of CO2 in seawater, giving the ocean has a vast capacity to store CO2. Currently the ocean holds about 50 times more inorganic carbon than the atmosphere, 99% of it in the form of HCO3-.
  However adding CO2 to seawater makes it more acidic, which reduces this "buffer capacity". Increasing the temperature also affects the chemical equilibria and reduces the solubility of CO2 in seawater. Both these feedbacks (acidification and temperature) act to decrease the future ocean sink.
  If you select "linear" from the @carbchemmenu (expert level) you will switch off the acidification effect.
  If you disable the @chemfbopt you will switch off the feedback from temperature. You may observe that this removes the spikes in the historical ocean sink, which are caused by equivalent spikes in radiative forcing, especially volcanos.
  (see also @flowchart )