1 Introduction
1.1 Purpose

1.2 Overall description of the system with its components
1.2.1 The system
1.2.2 Simulated processes
1.2.3 Modules and options

2 Development
2.1 The simulated events
2.1.1 Phenological stages
2.1.2 Leaf development

2.2 Emergence and initiation of crop development and growth
2.2.1 Emergence of sown crops
2.2.2 Onset of crop development and growth after planting
2.2.3 Onset of crop development and growth in perennial plants

2.3 Above-ground development
2.3.1 Time scale
2.3.2 Positive effect of temperature
2.3.3 Effect of photoperiod
2.3.4 Cold requirements
2.3.5 Effect of stress

3 Shoot growth
3.1 Leaf dynamics
3.1.1 Leaf area growth
3.1.2 Senescence
3.1.3 Photosynthetic function of storage organs
3.1.4 Use of ground cover instead of the leaf area index
3.1.5 Number of leaves
3.1.6 Green leaf specific area

3.2 Radiation interception
3.2.1 Beer's law and calculation of height
3.2.2 Radiation transfers and plant shape
3.3 Shoot biomass growth

3.3.1 Influence of radiation and phasic development
3.3.2 Effect of atmospheric CO2 concentration
3.3.3 Remobilisation of reserves
3.3.4 Calculation of the source/sink ratio
3.3.5 Height-biomass conversion

3.4 Stress indices
3.4.1 Water deficiency
3.4.2 Nitrogen deficiency
3.4.3 Trophic stress
3.4.4 Temperature stresses
3.4.5 Waterlogging
3.4.6 Stresses directly linked to the soil structure
3.4.7 Interactions between stresses

3.5 Partitioning of biomass in organs
3.5.1 Organs and compartments identified.
3.5.2 Dimensioning of organs
3.5.3 Harvested organs
3.5.4 Reserves

4 Yield formation
4.1 For determinate growing plants

4.2 For indeterminate growing plants
4.2.1 Fruit setting
4.2.2 Fruit filling

4.3 Quality
4.3.1 Water content of organs
4.3.2 Biochemical composition

5 Root growth
5.1 Root front growth

5.2 Growth in root density
5.2.1 Standard profile
5.2.2 True density
5.2.3 Comparison of the two kinds of density profiles

6 Management and crop environment
6.1 Effects on plants
6.1.1 Planting design
6.1.2 Simulation of the decision to sow
6.1.3 Yield regulation
6.1.4 Harvest
6.1.5 Pruning

6.2 Soil water supply
6.2.1 Irrigation
6.2.2 Interception of water by foliage

6.3 Net nitrogen supply
6.3.1 N inputs from rain and irrigation
6.3.2 N inputs from mineral fertilisers
6.3.3 N inputs from organic residues
6.3.4 Crop residues for the following crop

6.4 Physical soil surface conditions
6.4.1 Quantity of plant mulch and proportion of soil cover
6.4.2 Surface run-off
6.4.3 Modification to water balance induced by the mulch
6.4.4 Modification of crop and soil temperatures by the presence of a mulch
6.4.5 Influence of soil crusting on emergence

6.5 Soil structure modification
6.5.1 The soil structure in STICS
6.5.2 Compaction as influenced by sowing and harvesting machines
6.5.3 Fragmentation under the effects of soil tillage implements

6.6 Microclimate
6.6.1 Calculation of net radiation
6.6.2 Calculation of crop temperature
6.6.3 Calculation of the canopy moisture
6.6.4 Estimation of microclimate under shelter

7 Water Balance
7.1 Soil evaporation
7.1.1 Potential evaporation
7.1.2 Actual evaporation
7.1.3 Distribution in the soil profile

7.2 Plant water requirements
7.2.1 The crop coefficient approach
7.2.2 The resistance approach

7.3 Plant transpiration and derived stresses
7.3.1 Actual transpiration
7.3.2 Extrapolation to the water stress turgor index
7.3.3 Distribution of root water extraction within the profile

8 Nitrogen transformations
8.1 Mineralization of soil organic matter

8.2 Mineralization of organic residues

8.3 Nitrification

8.4 Ammonia volatilization

8.5 Denitrification

8.6 Nitrogen uptake by plants and plant nitrogen status
8.6.1 The dilution curves
8.6.2 The N supply from the soil
8.6.3 The N uptake capacity
8.6.4 The actual N uptake

8.7 Nitrogen fixation by legumes
8.7.1 The potential N2 fixation
8.7.2 The actual N2 fixation

9 Transfers of heat, water and nitrates
9.1 Soil temperature

9.2 Transfers of water and nitrates in undrained soil
9.2.1 Soil compartmentation
9.2.2 Soil microporosity: basis for calculating water and nitrogen transfer values
9.2.3 Pebbles
9.2.4 Macroporosity and cracks

9.3 Case of drained soil

9.4 Integrated calculations of soil status
9.4.1 Water and nitrogen reserves
9.4.2 Water and nitrogen balances
9.4.3 Predawn plant water potential

10 Cropping systems
10.1 The notion of a Unit of SiMulation (USM)

10.2 Long term simulations
10.2.1 Monocrop vs rotations
10.2.2 The particular case of crop residues
10.2.3 Examples of long term simulations

10.3 Intercropping
10.3.1 Representation of the intercropping system
10.3.2 The radiation intercepted by the two crops
10.3.3 Energy budget and microclimate
10.3.4 Leaf growth of the understorey crop
10.3.5 Root profiles
10.3.6 Simulation examples

11 Involvement of the user in the model operation
11.1 Driving options
11.1.1 Regular weather driving variables
11.1.2 Driving the model by weather data for high altitude climates
11.1.3 Driving the model by observed stages
11.1.4 Driving the model by the LAI

11.2 Simulation options
11.2.1 Water or nitrogen stress activation or deactivation
11.2.2 Smoothing of initial profiles
11.2.3 Long term simulations (see $ 10.2)

11.3 Formalisation options

11.4 Parameterization
11.4.1 Plant parameterization
11.4.2 Soil parameterization
11.4.3 Crop management parameterization

12 References

13 Figure list

14 Table list

15 Definitions of symbols

16 Index of parameters and variables