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Representation of vegetation in LPJ: The concept of Plant Functional Types (PFTs).

Classification of plants based on functional differences (PFTs, CFTs, BFTs and sub-classes).
Representation of plants types based on functional structures (pools) and traits (parameters).

The idea of plant functional types (PFTs) is to represent the various plant species as a small number of discrete representatives, which captures the most important differences in terms of plant strategies (evergreen vs. deciduous). All differences between species grouped within a PFT are assumed to be unimportant for the dynamics modeled (vegetation dynamics, carbon and water cycle). [Boris may have something to add here]. A paper on the idea of plant functional types and their limitations can be found here:
http://onlinelibrary.wiley.com/doi/10.1029/2010JG001430/full

11 plant functional types are defined in the parameter file source:trunk/par/pft.par (in directory LPJROOT/par) in the following order:

1. Tropical broadleaved evergreen tree
2. Tropical broadleaved raingreen tree
3. Temperate needleleaved evergreen tree
4. Temperate broadleaved evergreen tree
5. Temperate broadleaved summergreen tree
6. Boreal needleleaved evergreen tree
7. Boreal broadleaved summergreen tree
8. Boreal needleleaved summergreen tree
9. Tropical herbaceous (C4)
10. Temperate herbaceous (C3)
11. Polar herbaceous (C3)

They are differentiated by physiological, morphological, phenological, bioclimatic and fire-response attributes.
Photosynthesis is calculated daily, while PFT population densities are updated annually.
PFTs can be mixed within a stand.

BFT = Bioenergy Functional Type

1. Bioenergy tropical tree
2. Bioenergy temperate tree
3. Bioenergy C4 grass

CFT = Crop Functional Type

1. Temperate cereals
2. Rice
3. Maize
4. Tropical cereals
5. Pulses
6. Temperate roots
7. Tropical roots
8. Oil crops sunflower
9. Oil crops soybean
10. Oil crops groundnut
11. Oil crops rapeseed
12. Sugarcane
    (13. others)

PFT-specific output files defined in source:trunk/par/outputvars.par are:

id	name	variable(NetCDF)	description	unit	scale
PFT_NPP	pft_npp	NPP	PFT-specific NPP	gC/m2/yr	1.0
PFT_GCGP	pft_gcgp	GCGP	PFT-specific water stress		1.0
PFT_HARVEST	pft_harvest	harvest	harvested carbon	gC/m2/yr	1.0
PFT_RHARVEST	pft_rharvest	rharvest	harvested residual carbon	gC/m2/yr	1.0
PFT_AIRRIG	pft_airrig	PFT_irrig	CFT-specific irrigation	mm/yr	1.0

These can be grid-scaled or not. For grid-based output, set WITH_GRIDBASED in the LPJmL .conf file. Then the stand fraction (for PFTs) and the cftfrac (for CFTs) is multiplied with the output data.
Note that only PFT_NPP and PFT_GCGP contain natural vegetation. These outputs have 43 bands, the others have 32 bands.

Note that the output file for the fractional projective cover fpc.nc contains the following 12 bands (1 nat_veg_fraction + 11 PFT types):

1 fraction natural vegetation (<1 when with landuse)
2 Tropical broadleaved evergreen tree
3 Tropical broadleaved raingreen tree
4 Temperate needleleaved evergreen tree
5 Temperate broadleaved evergreen tree
6 Temperate broadleaved summergreen tree
7 Boreal needleleaved evergreen tree
8 Boreal broadleaved summergreen tree
9 Boreal needleleaved summergreen tree
10 Tropical herbaceous (C4)
11 Temperate herbaceous (C3)
12 Polar herbaceous (C3)

In the pft_outputs, the order of the PFTs is as follows:

natural PFTs
1 Tropical broadleaved evergreen tree
2 Tropical broadleaved raingreen tree
3 Temperate needleleaved evergreen tree
4 Temperate broadleaved evergreen tree
5 Temperate broadleaved summergreen tree
6 Boreal needleleaved evergreen tree
7 Boreal broadleaved summergreen tree
8 Boreal needleleaved summergreen tree
9 Tropical herbaceous (C4)
10 Temperate herbaceous (C3)
11 Polar herbaceous (C3)

Rainfed CFTs
12 Temperate cereals (wheat, rye, barley; wheat)
13 Rice (paddy rice; rice)
14 Maize (maize for food; maize)
15 Tropical cereals (millet, sorghum; millet)
16 Pulses (pulses; field peas)
17 Temperate roots (sugar beet; sugar beet)
18 Tropical roots (cassava; cassava)
19 Sunflower (sunflower; sunflower)
20 Soybean (soybean; soybean)
21 Groundnuts (groundnuts; groundnuts)
22 Rapeseed (rapeseed; rapeseed)
23 Sugarcane (sugarcane: sugarcane)
24 others (potatoes, oil palm, citrus, date palm, grapes/vine, cotton, cocoa, coffee, other perennial crops, other annual crops; managed grassland)
25 managed grasslands (pastures; managed grasslands)
26 bio-energy grass
27 bio-energy tree

Irrigated CFTs (the same as above)
28 Temperate cereals (wheat, rye, barley; wheat)
29 Rice (paddy rice; rice)
30 Maize (maize for food; maize)
31 Tropical cereals (millet, sorghum; millet)
32 Pulses (pulses; field peas)
33 Temperate roots (sugar beet; sugar beet)
34 Tropical roots (cassava; cassava)
35 Sunflower (sunflower; sunflower)
36 Soybean (soybean; soybean)
37 Groundnuts (groundnuts; groundnuts)
38 Rapeseed (rapeseed; rapeseed)
39 Sugarcane (sugarcane: sugarcane)
40 others (potatoes, oil palm, citrus, date palm, grapes/vine, cotton, cocoa, coffee, other perennial crops, other annual crops; managed grassland)
41 managed grasslands (pastures; managed grasslands)
42 bio-energy grass
43 bio-energy tree