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LPJmL includes 3 carbon pools (and corresponding sub-compartments) which are available as outputs: vegetation, litter and soil.

The vegetation carbon pool integrates all carbon stored in the standing biomass. It is the sum over all PFT-specific tissue pools: leaves, sapwood, heartwood and fine roots for woody plant functional types (PFTs); leaves and fine roots for herbacious PFTs; and leaves, fine roots, harvestable storage organ and a pool representing stems and mobile reserves for crop functional types (CFTs). Carbon enters the vegetation carbon pool by the process of allocation of NPP. Several processes remove carbon from the vegetation pool: fire, harvest, land-use change, mortality, turnover.

Litter carbon pools are kept on a stand basis. Turnover and mortality transfer carbon from the vegetation to the litter pool of the same stand. Litter pools are PFT specific for the aboveground part and are created with establishment of the corresponding plants. src/soil/addlitter.c (Litter pools that have been created once do continue to exist even if the respective PFTs are not present anymore). There is one belowground (bg) litter pool. The aboveground (ag) component consists of one litteritem per PFT. The litteritem has a pointer to the corresponding PFT-parameters and a trait, which consists of a leaf litter pool and various wood litter pools that are distinguished by fuel classes. See source:trunk/include/soil.h
Decomposition of soil organic matter (SOM) in the litter pools is computed in src/soil/littersom.c. A linear decay function is also implemented technically (compile with pre-compiler switch LINEAR_DECAY), but the default setting has an exponential decay function.
There is a slow and a fast decaying pool of litter.

Litter pools are PFT-specific following the publication by Brovkin et al. (2012): Plant-driven variation in decomposition rates improves projections of global litter stock distribution

Soil carbon stocks are kept on a stand basis. Litter decomposition feeds carbon into the atmosphere, and slow and fast soil carbon pools. Soil carbon pools are distributed over the [soil](soil layers) by layer-specific shift rates, see src/soil/equilsoil.c#L155 ff.
Decomposition of soil organic matter (SOM) is computed in src/soil/littersom.c. A linear decay function is also implemented technically (compile with pre-compiler switch LINEAR_DECAY), but the default setting has an exponential decay function.
There is a slow and a fast decaying pool of soil.

In terms of LPJmL output files (.bin or .nc), the balance equations are:

Carbon storage = vegC + litC + soilC
Carbon sequestration = mnpp + flux_estab + pft_rharvest - rh - fireC - flux_harvest - deforest_emissions

The difference in carbon storage over 1 year must equal the carbon sequestration in the same time period.

heterotrophic respiration