README

Skeleton of pyAPES -multi-layer soil-plant-atmosphere model. Original version used for simplified model: pyAPES_kersti master (v. 12.11.2019).

Samuli Launiainen 12.11.2019

Introducing clear and consistent interfaces throughout the model code

run function arguments:

• forcing: forcing data
• parameters: previously calculated states
• controls: control flags, needed parameters etc.

run function returns a dict containing states and fluxes of encapsulated submodels to be used in upper-level.

Migration to Python3

https://docs.python.org/3.0/whatsnew/3.0.html Code is mainly written so that it works in both python 2.7 and 3.6 (should run versions >3.5)

• main things:
  • in python3, print is a function; brackets are needed
  • iterating a list: if a index is needed use enumarate() then list(range(len(foo))) is not needed. e.g. 'for index, item in foo:' instead of 'for index in list(range(len(foo))):'
  • iterating a dict: if you are iterating through dict.items(), dict.keys(), and dict.values() AND adding/deleting item from dict wrap it inside a list(). e.g. 'for key in list(dict.keys()): del dict[key]'.
  • absolute import vs. relative import: from .foo import spam if you want to import from same package.

SoilProfile

Water flow:

• Equilibrium within vertical column during each timestep
• OR Richards 1D equation ! problem with infiltration (pF curves and unsaturated hydraulic conductivity) ! description of preferential flow?

Heat flow:

• solves heat conduction -> soil temperature and ice content ! neglects heat convection (heat transfer with water flow)

Canopy

Multilayer canopy description

• Radiation model: canopy SW (PAR&NIR) and LW including multiple scattering in horizontally homogenous porous media Zhao & Qualls (2005, 2006), sunlit/shade leaves ! range of zenith angle?
• Interception model: interception of rainfall and snow following approach by Tanaka (2002, Ecol. Mod.) -> solves wet leaf temperature ! restrict to snow surface level? sublimation of snow from canopy should be checked
• Leaf gas-exchange: Photosynthesis calculated based on biochemical model of Farquhar et al. (1980) coupled with various stomatal control schemes (Medlyn, Ball-Woodrow-Berry, Hari, Katul-Vico et al.) -> solves dry leaf temperature
• Momentum, H2O, CO2 and T within canopy: 1st-order closure model (sources/sinks: evaporation, transpiration, photosynthesis, respiration, sensible heat etc.)

Forest floor and snowpack:

• Moss cover (present during snow free periods): Interceps rainfall and evaporates interception storage, CO2 exchange (respiration and photo?) ! capillary flux not included
• Bare soil surface energy balance -> solves soil surface temperature
• Soil respiration ! simplified?
• Snow model: Temperature-based snow accumulation and melt In future two layer energy balance snow scheme + soil freezing thawing (FEMMA)?

Forcing

Lettosuo (2010-2018) Hyytiälä (1997-2016) see tools/dataprocessing_scripts

Todos..

• Documentation!
• Updating bryophyte model (energy and water)
• Description of soil respiration? branches etc..
• Marklund biomass functions ok for drained peatlands?
• Feedbacks from soil to canopy
• Parallelize model run and result writing (netCDF4) as in Climoss
• Running sensitivity analysis easily?