The medfate book
Preface
How to use this book
An collaborative project
Funding
History and acknowledgements
I Preliminaries
1
Introduction
1.1
Purpose
1.1.1
Package medfate
1.1.2
Package medfateland
1.1.3
Companion packages
1.2
Installation
1.2.1
Requirements
1.2.2
Installing medfate
1.2.3
Installing medfateland
1.3
Main functions in medfate
1.3.1
Dynamic simulation functions
1.3.2
Sub-model functions
1.3.3
Static functions
1.4
Main functions in medfateland
2
Model inputs
2.1
Input structures
2.1.1
Input structures in medfate
2.1.2
Input structures in medfateland
2.2
Latitude and topography
2.3
Soil description
2.3.1
Soil physico-chemical properties
2.3.2
Water retention curves
2.3.3
Soil initialization
2.3.4
Water content and depth to saturation
2.4
Vegetation description
2.4.1
Cohorts of living plants
2.4.2
Forest objects
2.4.3
Leaf and root distribution
2.4.4
Functional traits and vegetation initialization
2.4.5
Update of vegetation during simulations
2.5
Metereological input
2.5.1
Date format
2.5.2
Required weather variables
2.5.3
Optional weather variables
2.5.4
Derived weather variables
2.6
Simulation control
II Basic water balance modelling
3
Basic water balance model
3.1
Design principles
3.2
State variables
3.3
Water balance
3.4
Process scheduling
3.5
Inputs and outputs
3.5.1
Soil, vegetation and meteorology
3.5.2
Vegetation functional parameters
3.5.3
Control parameters
3.5.4
Model output
3.6
Applications
4
Leaf phenology and radiation extinction
4.1
Leaf phenology
4.1.1
Phenological types and leaf expanded area
4.1.2
Bud burst and leaf unfolding
4.1.3
Leaf senescence
4.1.4
Leaf abscission
4.2
Radiation extinction
5
Forest hydrology
5.1
Snow and rainfall
5.2
Snow pack dynamics
5.3
Rainfall interception loss
5.3.1
Gash (1995) model
5.3.2
Liu (2001) model
5.4
Bare soil evaporation
5.5
Transpiration of the herbaceous layer
5.6
Infiltration
5.6.1
Boughton (1989) model
5.6.2
Green-Ampt (1911) model
5.7
Soil water flows
5.7.1
Design of soil water flows
5.7.2
Darcian flow and Richards equation
5.7.3
Hydraulic properties in the single-domain model
5.7.4
Hydraulic properties in the dual-permeability model
5.7.5
Finite approximation to flows in the soil matrix
5.7.6
Finite approximation to flows in the macropore domain
6
Plant cohort transpiration, photosynthesis and water status
6.1
Plant transpiration and photosynthesis
6.1.1
Maximum transpiration
6.1.2
Actual plant transpiration and plant water potential
6.1.3
Plant water potential
6.1.4
Minimum transpiration
6.1.5
Transpiration with water pools
6.1.6
Plant photosynthesis
6.2
Plant drought stress and cavitation
6.2.1
Daily drought stress
6.2.2
Cavitation and hydraulic recovery
III Advanced water balance modelling
7
Advanced water balance model
7.1
About Sureau
7.2
Design principles
7.3
State variables
7.4
Water and energy balances
7.4.1
Water balance
7.4.2
Single-layer canopy energy balance
7.4.3
Multiple-layer canopy energy balance
7.4.4
Soil energy balance
7.5
Process scheduling
7.6
Inputs and outputs
7.6.1
Soil, vegetation and meteorology
7.6.2
Vegetation functional parameters
7.6.3
Control parameters
7.6.4
Model output
7.7
Applications
8
Sub-daily atmospheric temperature and radiation variation
8.1
Above-canopy air temperature
8.2
Incoming diffuse and direct short-wave radiation
8.3
Incoming long-wave radiation
9
Radiation transfer
9.1
Short-wave radiation
9.1.1
Direct and diffuse irradiance across the canopy
9.1.2
Sunlit and shade leaves
9.1.3
Short-wave radiation absorbed by canopy elements
9.1.4
Short-wave radiation absorbed by the soil
9.2
Long-wave radiation
9.2.1
Long-wave radiation balance by canopy layers
9.2.2
Net long-wave radiation of the whole canopy and the soil
9.2.3
Long-wave radiation balance by plant cohorts
10
Plant hydraulics
10.1
Hydraulic architecture
10.2
Vulnerability curves
10.2.1
Xylem vulnerability curves
10.2.2
Rhizosphere vulnerability curve
10.2.3
Xylem sap viscosity
10.3
Water content of plant tissues
10.3.1
Relative water content of symplasmic tissues
10.3.2
Relative water content of apoplastic tissues
10.3.3
Average relative water content of a compartment
10.3.4
Live fuel moisture content
10.4
Sperry’s sub-model of plant hydraulics
10.4.1
Supply function for a single xylem element
10.4.2
Supply function of two elements in series
10.4.3
Supply function of three elements in series
10.4.4
Supply function of a root system
10.4.5
Supply function of the soil-plant continuum
10.5
Sureau’s sub-model of plant hydraulics
10.5.1
Constitutive equations
10.5.2
Plant and soil conductances
10.5.3
Plant capacitances
10.5.4
Cavitation flows
10.5.5
Transpiration flows
10.5.6
Numerical scheme
11
Leaf/canopy photosynthesis
11.1
Leaf energy balance, gas exchange and photosynthesis
11.1.1
Leaf temperature
11.1.2
Leaf vapor pressure deficit
11.1.3
Leaf gas exchange
11.1.4
Leaf photosynthesis
11.2
Crown/canopy photosynthesis
11.2.1
Multi-layer canopy photosynthesis model
11.2.2
Big-leaf canopy photosynthesis model
11.2.3
Sun-shade canopy photosynthesis model
11.2.4
Within-canopy variation in environmental conditions
12
Stomatal regulation, transpiration and photosynthesis
12.1
Stomatal regulation, transpiration and photosynthesis under Sperry’s sub-model
12.1.1
Water supply function
12.1.2
From water supply to sunlit/shade photosynthesis functions
12.1.3
Leaf stomatal regulation by profit maximization
12.1.4
Plant-level transpiration rates and plant water potentials
12.2
Stomatal regulation, transpiration and photosynthesis under Sureau’s sub-model
12.2.1
Transpiration flows
12.2.2
Cuticular conductances
12.2.3
Stomatal conductance
12.2.4
Photosynthesis
12.3
Scaling of transpiration, soil water uptake and photosynthesis rates
13
Closing energy balances
13.1
Single-layer canopy
13.1.1
Latent heat
13.1.2
Convective energy
13.1.3
Canopy temperature changes
13.1.4
Soil temperature changes
13.2
Multi-layer canopy
13.2.1
Latent heat of vaporization
13.2.2
Sensible heat between leaves and the canopy air space
13.2.3
Turbulent heat exchange
13.2.4
Canopy and soil temperature changes
13.2.5
Within-canopy changes in water vapor and
\(CO_2\)
14
Day-level results
14.1
Photosynthesis and transpiration
14.2
Plant water potentials and relative water contents
14.3
Plant drought stress
14.4
Cavitation and conduit refilling
IV Forest growth modelling
15
Forest growth model
15.1
Design principles
15.1.1
Overview
15.1.2
Plant carbon pools and carbon flows
15.1.3
Tissue growth, senescence and allocation
15.1.4
Update of structural variables
15.1.5
Plant mortality
15.1.6
Fire occurrence, severity and emissions
15.1.7
Organic matter decomposition
15.2
State variables
15.2.1
State variables related to live plant cohorts
15.2.2
State variables related to carbon decomposition
15.3
Mass and energy balances
15.3.1
Water and energy balance
15.3.2
Labile carbon balance
15.3.3
Plant biomass balance
15.3.4
Mass balance of decomposition pools
15.3.5
Fire combustion
15.3.6
Stand-level carbon balance
15.4
Process scheduling
15.5
Inputs and outputs
15.5.1
Soil, vegetation and meteorology
15.5.2
Vegetation functional parameters
15.5.3
Control parameters
15.5.4
Model output
16
Plant carbon pools and components of the labile carbon balance
16.1
Size of plant carbon pools
16.1.1
Leaf structural, dead, metabolic and storage biomass
16.1.2
Twig structural and dead biomass
16.1.3
Sapwood structural, metabolic and storage biomass
16.1.4
Heartwood biomass
16.1.5
Fine root area and biomass
16.1.6
Total living biomass
16.2
Components of labile carbon balance
16.2.1
Gross photosynthesis
16.2.2
Maintenance respiration
16.2.3
Growth costs and synthesis respiration
16.2.4
Phloem transport
16.2.5
Sugar-starch dynamics
16.2.6
Root exudation
17
Growth, senescence and mortality
17.1
Growth
17.1.1
Temperature and turgor sink limitations
17.1.2
Leaf growth
17.1.3
Sapwood growth
17.1.4
Fine root growth
17.2
Senescence
17.2.1
Leaf senescence and cavitation effects on leaves and buds
17.2.2
Sapwood senescence
17.2.3
Fine root senescence
17.3
Update of plant traits and allocation targets
17.3.1
Plant traits
17.3.2
Leaf area and fine root biomass targets
17.4
Update of structural variables
17.4.1
Tree diameter, height and crown ratio
17.4.2
Shrub height and cover
17.5
Plant mortality
17.5.1
Self-thinning of small trees
17.5.2
Basal mortality rates
17.5.3
Mortality due to starvation
17.5.4
Mortality due to dessication
17.5.5
Overall mortality probability
17.6
Fire severity
17.6.1
Plume temperature distribution
17.6.2
Foliage and crown bud necrosis
17.6.3
Cambium necrosis
18
Decomposition and soil biogeochemistry
18.1
Decomposition of standing dead wood and litter elements
18.2
Dynamics of soil carbon pools
V Forest dynamics modelling
19
Forest dynamics model
19.1
Design principles
19.1.1
Recruitment from seeds
19.1.2
Resprouting
19.1.3
Forest management
19.2
State variables
19.3
Process scheduling
19.4
Inputs and outputs
19.4.1
Soil, vegetation and meteorology
19.4.2
Vegetation functional parameters
19.4.3
Control parameters
19.4.4
Model output
19.5
Applications
20
Regeneration
20.1
Seed production and seed bank dynamics
20.2
Recruitment from seeds
20.3
Resprouting
VI Landscape/regional modelling
21
Watershed hydrology
21.1
Design principles
21.2
State variables
21.3
Water balance
21.3.1
Cell level water balance
21.3.2
Watershed water balance
21.4
Process scheduling
21.5
Inputs and outputs
21.5.1
Gridded inputs
21.5.2
Watershed meteorology input
21.5.3
Watershed hydraulic control parameters
21.5.4
Model outputs
21.6
Process details
21.6.1
Soil saturated lateral flow
21.6.2
Groundwater lateral flow
21.6.3
Overland runoff
21.6.4
Channel routing and water exported from the watershed
21.6.5
Losses towards a deeper aquifer
22
Seed dispersal
22.1
Design principles
22.2
Process scheduling
22.3
Process details
VII Static modules
23
Allometric models
23.1
Input data
23.1.1
Forest plot data
23.1.2
Species parameters
23.2
Allometric relationships
23.2.1
Leaf biomass
23.2.2
Leaf area and LAI
23.2.3
Crown vertical dimensions
24
Post-simulation procedures
24.1
Water use efficiency
25
Wind extinction
25.1
Wind speed at the top of the canopy
25.2
Wind extinction profile
26
Fuel characteristics and fire behaviour
26.1
Overview
26.2
Input data
26.2.1
Forest plot data
26.2.2
Species parameters
26.2.3
Other inputs
26.3
Fuel characteristics
26.3.1
Fuel strata
26.3.2
Cohort fuel loading
26.3.3
Vertical distribution of cohort fuels
26.3.4
Fuel bulk density profile
26.3.5
Fuel loading (
\(w\)
) and fuel depth (
\(\delta\)
)
26.3.6
Other fuel characteristics
26.3.7
Unit conversion of fuel characteristics
26.4
Surface fire behavior
26.4.1
Surface rate of spread (
\(R\)
)
26.4.2
Heat sink (
\(q\)
)
26.4.3
Fireline intensity (
\(I_B\)
) and flame length (
\(FL\)
)
26.5
Crown fire behavior
26.5.1
Canopy reaction intensity (
\(I_{R, ca}\)
)
26.5.2
Canopy heat sink (
\(q_{ca}\)
)
26.5.3
Fireline intensity (
\(I_{B,crown}\)
) and flame length (
\(FL_{crown}\)
)
26.6
Fire potentials
26.6.1
Surface fire behavior potentials
26.6.2
Crown fire behavior potentials
26.7
Unit conversion of outputs
26.8
Applications
Appendices
A
Inbuilt parameter estimation
A.1
Introduction
A.2
Strict, scaled and imputable parameters
A.3
Imputation of missing values
A.3.1
Rooting depth
A.3.2
Shrub allometric coefficients
A.3.3
Tree allometric coefficients
A.3.4
Leaf width, specific leaf area and fine foliar ratio
A.3.5
Tissue density
A.3.6
Specific root length and root length density
A.3.7
Huber value and ratio of conduits to sapwood
A.3.8
Fine root to leaf area ratio
A.3.9
Leaf phenology
A.3.10
Basic transpiration and water-use efficiency
A.3.11
Radiation balance and water interception
A.3.12
Stomatal conductance
A.3.13
Pressure-volume curves
A.3.14
Stem and root maximum hydraulic conductivity
A.3.15
Leaf maximum hydraulic conductance
A.3.16
Xylem vulnerability
A.3.17
Photosynthesis rates
A.3.18
Maintenance respiration rates
A.3.19
Relative growth rates
A.3.20
Senescence rates
A.3.21
Relative starch for sapwood growth
A.3.22
Wood carbon
A.3.23
Mortality baseline rate
A.3.24
Recruitment
A.3.25
Flammability
A.4
Scaling size-related parameters
A.4.1
Stem xylem maximum conductance
A.4.2
Leaf maximum hydraulic conductance
A.4.3
Root xylem maximum hydraulic conductance
A.4.4
Rhizosphere maximum hydraulic conductance
A.4.5
Plant water storage capacity
A.4.6
Horizontal root overlap
B
Symbols
B.1
Dimensions
B.2
Soils
B.3
Plant/leaf classification
B.4
Vegetation
B.5
Meteorology
B.6
Anatomy
B.7
Radiation
B.8
Water balance
B.9
Energy balance
B.10
Forest hydrology
B.11
Plant hydraulics
B.12
Photosynthesis
B.13
Plant water content
B.14
Stomatal regulation
B.15
Carbon pools
B.16
Carbon balance
B.17
Growth, senescence and mortality
Bibliography
Published with bookdown
The medfate reference book
Chapter 18
Decomposition and soil biogeochemistry
TO BE WRITTEN
18.1
Decomposition of standing dead wood and litter elements
TO BE WRITTEN
18.2
Dynamics of soil carbon pools
TO BE WRITTEN