Copyright: NDICEA 4.23 Copyright © 1996-2000 Fons Habets
Citation: NDICEA 4.23 Copyright © 1996-2000 Fons Habets


Contents

Symbols	Formulas	Figures	Tables

Introduction

1	Model overview

2	Waterbalance

2.1	Soil pF-curve

2.2	Watertable

2.3	Field capacity

2.4	Capillary rise

2.5	Bypass flow

2.6	Crop cover

2.7	Evapotranspiration

2.8	Rooting depth

2.9	Root density

2.10	Calculation of waterbalance

3	Mineralisation

3.1	Rate of aging

3.2	Temperature correction factor

3.3	Moisture correction factor

3.4	pH correction factor

3.5	Texture correction factor

3.6	Cultivation effect

3.7	From carbon to nitrogen mineralisation

4	Nitrogen balance

4.1	Nitrogen deposition

4.2	Nitrogen irrigation

4.3	Denitrification

4.4	Nitrogen uptake

4.5	Nitrogen fixation

4.6	Nitrogen matrixflow

4.7	Nitrogen bypassflow

References

Publications

Appendix 1: Soils file format (*.soi)

Appendix 2: Crops file format (*.cro)

Appendix 3: Applications file format (*.app)

Appendix 4: Scenario file format (*.dat)

Appendix 5: Environment file format (*.env)

Appendix 6: Irrigation file format (*.irr)

Appendix 7: NMineral file format (*.min)


About
About NDICEA

Nitrogen Dynamics In Crop rotations in Ecological Agriculture.

Copyright © 1996-2000 Fons Habets

 About

Ndicea, a simple and easy to use nitrogen dynamics model.

You are free to try out Ndicea and use it for non commercial purposes. In any other case you have to register. See the section 'Registration' below for more information.

You are allowed to copy Ndicea and pass it around to anyone who may be interested, as long as you don't change any of the files and at the very most, charge a small media and handling fee.

 Copyright

The author reserves the exclusive right to distribute this program, or any part thereof, for profit.

 Disclaimer

This program is distributed as is, with no guarantee that it will work correctly in all situations. In no event will the author be liable for any damages, including lost profits, lost savings or other incidental or consequential damages arising out of the use of or inability to use this program, even if the author has been advised of the possibility of such damages, or for any claim by any other party. Also the author is not liable for the correctness of the data supplied with this program.

I would appreciate if any bugs, remarks or suggestions are brought to my attention.

 Registration

If you use the program in a commercial way or in a business you have to register (at a reasonable fee). Contact the author at the address below for registration. Registered users can also be informed of new versions and ask for support.

 Address

 Fons Habets

 Palenbergstraat 53

 NL 6415 RB HEERLEN

 E-mail: habets@cuci.nl


Tables

Table 1: Humificationcoëfficiënts and apparent initial age for some types of organic matter (Janssen, 1988)

Table 2: Average C/N and A/D quotient for some groups of micro-organisms (Hendriks,1992)


Figures

Figure 1: Schematic structure of model

Figure 2: Schematic representation 2-layer model.

Figure 3: Calculated pF-curves for some soiltypes.

Figure 4: Ground water table.

Figure 5: Distance to ground water table and maximum capillary rise for different soil types (Anonymus, 1989).

Figure 6: Crop cover at different crop development stages.

Figure 7: Crop rooting depth.

Figure 8: Water uptake factor at different soil pF.

Figure 9: Decomposition of 100 ton organic matter with different apparent initial age.

Figure 10: Relation between humification coefficient and apparent initial age.

Figure 11: Comparison of temperature correction factors.

Figure 12: Moisture correction factor.

Figure 13: Correction factor mineralisation by soil pH.

Figure 14: Flowdiagram from C to N mineralisation.

Figure 15: N-mineralisation of 100 ton organic matter with an initial age of 2.45 at different organic N content.


Formulas

Formula 1: Moisture content as a function of matrix suction.

Formula 2: Matrix suction as a function of moisture content.

Formula 3: Definition of soil pF value.

Formula 4: Redefinition of moisture content.

Formula 5: Ground water table.

Formula 6: Equilibrium matrix suction topsoil.

Formula 7: Equilibrium matrix suction subsoil.

Formula 8: Matrix suction at field capacity.

Formula 9: Moisture content at field capacity.

Formula 10: Maximum capillary rise topsoil.

Formula 11: Maximum capillary rise subsoil.

Formula 12: Bypassflow topsoil.

Formula 13: Differential flow subsoil.

Formula 14: Crop cover factor.

Formula 15: Intended crop evapotranspiration.

Formula 16: Crop rooting depth.

Formula 17: Root density.

Formula 18: Moisture content soil layers.

Formula 19: Matrixflow into topsoil.

Formula 20: Matrixflow into subsoil.

Formula 21: Capillary rise topsoil.

Formula 22: Capillary rise subsoil.

Formula 23: Water uptake factor.

Formula 24: Water uptake topsoil.

Formula 25: Water uptake subsoil.

Formula 26: Limitation of water uptake by wilting point.

Formula 27: Matrixflow out of soil layer.

Formula 28: Definition of effective organic matter.

Formula 29: Exponential decay with constant k.

Formula 30: Variable decayrate k according to Janssen.

Formula 31: Janssen's formula.

Formula 32: Relation between humification coefficient and apparent initial age.

Formula 33: Differential form of Janssen's formula.

Formula 34: Overall correction factor f for mineralisation rate.

Formula 35: Definition rate of aging.

Formula 36: Introduction of apparent age in Janssen's formula.

Formula 37: Refined differential form of Janssen's formula.

Formula 38: Organic matter mineralisation on yearly basis.

Formula 39: From yearly to weekly time scale.

Formula 40: Organic matter mineralisation on weekly basis.

Formula 41: Calculating apparent age.

Formula 42: Q9 temperature correction factor.

Formula 43: Arrhenius temperature correction factor.

Formula 44: Yang's temperature correction factor.

Formula 45: NDICEA temperature correction factor.

Formula 46: Moisture correction factor.

Formula 47: pH correction factor.

Formula 48: Carbon assimilation by micro organisms.

Formula 49: Carbon turnover by micro organisms.

Formula 50: Nitrogen assimilation by micro organisms.

Formula 51: Nitrogen turnover by micro organisms.

Formula 52: Current CN ratio organic matter.

Formula 53: From carbon to nitrogen mineralisation.

Formula 54: From organic matter to nitrogen mineralisation.

Formula 55: Nitrogen balance.

Formula 56: Nitrogen matrixflow into topsoil.

Formula 57: Nitrogen matrixflow into subsoil.

Formula 58: Deposition per week.

Formula 59: Denitrification.

Formula 60: Total crop nitrogen uptake.

Formula 61: Total crop nitrogen uptake minus seed.

Formula 62: Weighing factor for nitrogen uptake.

Formula 63: Intended nitrogen uptake.

Formula 64: Nitrogen uptake from topsoil.

Formula 65: Nitrogen uptake from subsoil.

Formula 66: Proportionality factor nitrogen uptake from topsoil and subsoil.

Formula 67: Intended nitrogen uptake A.

Formula 68: Intended nitrogen uptake B.

Formula 69: Modelled nitrogen uptake from the topsoil.

Formula 70: Modelled nitrogen uptake from the subsoil.

Formula 71: Intended weekly nitrogen fixation.

Formula 72: Reduced intended nitrogen fixation.

Formula 73: Nitrogen matrix flow out of soil layer.

Formula 74: Nitrogen matrix flow out of topsoil in case of capillary rise.

Formula 75: Nitrogen matrix flow out of subsoil in case of capillary rise.

Formula 76: Nitrogen bypass flow topsoil.

Formula 77: Differential nitrogen flow if differential water flow > 0.

Formula 78: Differential nitrogen flow if differential water flow < 0.


Symbols

a = Initial apparent age [years]

AC = Assimilation of carbon [kg/week]

ADmicro = Assimilation to dissimilation ratio micro organisms [-]

Age = Apparent age [years]

am = Molar activation energie = 47619 [J/mol]

AN = Assimilation of nitrogen [kg/week]

BPF = ByPass Flow factor: fraction bypass flow of total flow [-]

ByPassFlow = Bypass flow of water at soil layer [mm/week]

C = Amount of organic carbon [kg]

CC = Crop cover factor [-]

CN = Carbon to nitrogen ratio organic matter [-]

CNmicro = Carbon to nitrogen ratio micro organisms [-]

CR = Capillary rise into soil layer [mm/week]

CRc = Distance above water table where potential capillary rise is equal to 1 mm/day [cm]

CRmax = Maximum capillary rise [mm/week]

CRx = Distance above CRc where potential capillary rise decreases a factor e [cm]

DC = Dissimilation of carbon [kg/week]

DiffFlow = Differential flow from matrix to bypass flow [mm/week]

DMcProd = Dry matter content product [kg/kg]

DMcSeed = Dry matter content seed [kg/kg]

DN = Dissimilation of nitrogen [kg/week]

DN0 = Denitrification thresshold [kg N/ha]

DNF = Denitrification factor soil layer [kg/1000 kg OM/kg N]

ET0 = Reference crop evapotranspiration [mm/week]

ETbare = Evaporation factor bare soil [-]

ETmax = Maximum crop evapotranspiration factor [-]

f = Overall correction factor = rate of aging [-]

FI = Flow Intensity where bypass flow starts [mm/week]

FlowOut = Total flow out of soil layer [mm/week]

fNUPT = Weighing factor for weekly intended crop nitrogen uptake and fixation [-]

fpH = pH correction factor [-]

fProd = Fraction product | residue | root of total dry matter [-]

fResi = Fraction residues of total dry matter [-]

fRoot = Fraction roots of total dry matter [-]

fT = Temperature correction factor [-]

fTArrh = Arrhenius temperature correction factor [-]

fText = Texture correction factor [-]

fTheta = Moisture correction factor [-]

fTQ9 = Q9 temperature correction factor [-]

fTYang = Yang's temperature correction factor [-]

FullCover = Time when crop reaches maximum evapotranspiration factor and maximum rooting depth [weeks]

GAM = Coefficient influencing shape of soil pF curve: the higher the value the steeper the change of matrix suction with soil moisture content [/cm2]

GWT = Level of ground water table (cm)

GWT1 = First level of extreme ground water table (cm)

GWT2 = Second level of extreme ground water table (cm)

GWTwk1 = First week of extreme ground water table (week 1-52)

GWTwk2 = Second week of extreme ground water table (week 1-52)

h = Humification coëfficient [-]

Harvest = Time of crop harvest [weeks]

Irri = Irrigation [mm/week]

k = Decay rate [-]

M = Moisture content soil layer [mm]

MatrixFlowIn = Matrix flow of water into soil layer [mm/week]

MatrixFlowOut = Matrix flow of water out of soil layer [mm/week]

MFC = moisture content soil layer at field capacity [mm]

MWP = Moisture content soil layer at wilting point [mm]

MWU = Minimum Water Uptake fraction for maximum nitrogen uptake [-]

N = Nitrogen content soil layer [kg N/ha]

NByPassFlow = Nitrogen bypass flow at soil layer [kg N/ha/week]

NcProd = Nitrogen content in dry matter product [kg/kg]

NcResi = Nitrogen content in dry matter residues [kg/kg]

NcRoot = Nitrogen content in dry matter roots [kg/kg]

NcSeed = Nitrogen content in dry matter seed [kg/kg]

NDen = Denitrification in soil layer [kg N/ha/week]

NDep = Nitrogen deposition [kg N/ha/week]

NDiffFlow = Differential flow of nitrogen from matrix to bypass flow [kg N/ha/week]

NFix0 = Nitrogen fixation thresshold [kg N/ha in topsoil]

NFixCrop = Potential crop nitrogen fixation [kg N/ha]

NFixI = Intended crop nitrogen fixation [kg N/ha/week]

NGW = Nitrogen content ground water [mg/l]

NGW1 = First nitrogen content ground water (mg/l)

NGW2 = Second nitrogen content ground water (mg/l)

NIrri = Nitrogen irrigation [kg N/ha/week]

NMatrixFlowIn = Nitrogen matrix flow into soil layer [kg N/ha/week]

NMatrixFlowOut = Nitrogen matrix flow out of soil layer [kg N/ha/week]

NMin = Nitrogen mineralization soil layer [kg N/ha/week]

NUpt = Modelled nitrogen uptake from soil layer [kg N/ha/week]

NUptCrop = Total intended crop nitrogen uptake [kg N/ha]

NUptI = Intended crop nitrogen uptake [kg N/ha/week]

OM = Organic matter in soil layer [kg]

ON = Organic nitrogen [kg]

p = Proportionality between water uptake, nitrogen concentration and N-uptake [-]

pF = pF value soil layer [-]

pFGWT = pF soil layer at equilibrium matrix suction [-]

pH = Acid value soil layer [-]

Prod = Quantity of crop product yield [kg/ha]

psi = Matrix suction soil layer (cm)

psiFC = Matrix suction soil layer at field capacity [cm]

psiGWT = Equilibruim matrix suction = distance of center of layer to watertable [cm]

R = Gas constante = 8.314 [J/mol/K]

Rain = Rainfall [mm/week]

RD = Rooting depth [cm]

RDmax = Maximum crop rooting depth [cm]

Resi = Quantity of crop residues [kg/ha]

RF = Fraction of all roots in soil layer [-]

Ripening = Time when ripening starts [weeks]

Root = Quantity of crop roots [kg/ha]

Seed = Quantity of seed or planting material [kg/ha]

SMO = Saturated soil moisture content (m3/m3)

Sowing = Time of planting or crop emergence [weeks]

t = Time variable [weeks]

T = Temperature [oC]

TC = Turnover of carbon [kg/week]

Theta = Moisture content soil layer (m3/m3)

THL = Thickness soil layer [cm]

TK = Temperature [Kelvin]

TKref = Reference temperature [Kelvin]

TN = Turnover of nitrogen [kg/week]

Tref = Reference temperature [oC]

Upt = Modelled water uptake from soil layer [mm/week]

UptI = Intended water uptake [mm/week]

WoY = Time variable (week of year 1-52)

WUF = Water uptake reduction factor [-]

y = Time variable [years]


Introduction

See also	Symbols	Formulas	Figures	Tables

Nitrogen plays a major role in plant production. Every soil contains a lot of nitrogen, though mainly not readily available for plant uptake. Many processes and factors determine how much nitrogen comes available and which part of this is actually taken up by a crop, or lost by leaching or denitrification.

Even when the single processes and factors are largely understood, in practice it is difficult to see through the interactions and realise a good management of nitrogen resources.

On the basis of experience, or long term experiments, effects of changes in farm management on nitrogen dynamics can be determined. But it may still be difficult to understand gathered knowledge and apply it to other specific conditions and other farms.

A model that integrates the most important processes and factors can help here. NDICEA has been, and is being, used by students and researchers in several projects. It can supply more insight in the complexity of the nitrogen dynamics, show the importance of and relation between different processes and act as a generator/tester of ideas.

NDICEA is not perfect and it doesn't need to be. With feed back from the 'field' the model keeps developing. In future I hope the model can be used as a reliable tool, not only in research, but also by farmers, in solving some of their practical problems.


Introduction: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Nitrogen balance

References

Publications


Model overview
1 Model overview

See also	Symbols	Formulas	Figures	Tables

NDICEA is a simple two layer model, with a timestep of a week, to study the availability of nitrogen in a crop rotation. The model includes a waterbalance, with capillary rise and bypass flow, to estimate soil moisture content and water leaching. Mineralisation of initial soil organic matter and of the consecutive additions of crop residues and organic manure to the soil are calculated taking account of temperature, soil moisture content, soil texture and soil pH. Crop nitrogen uptake is based on actual yield data, and estimated amounts and nitrogen contents of crop residues and roots. The mineral nitrogen balance includes mineralisation, deposition, irrigation, denitrification, fixation, uptake, capillary rise and leaching.

Figure 1: Schematic structure of model

Core of the model is the description of mineralisation by Janssen's formula (Janssen, 1984). For every single addition the course of mineralisation is calculated, depending on the quantity and type of organic matter. A correction to the formula is applied for soil temperature, soil moisture, soil texture and soil pH. Soil temperatures can be obtained from the nearest weather station. Soil moisture is calculated with a simple waterbalance using rainfall and evapotranspiration figures from the weather station and soil properties.

The total quantity of plant available nitrogen is determined by soil depth and rooting depth. The plant takes up nitrogen from this stock and incorporates it in different parts. A part of the plant will be harvested, an other part is left behind in the field. Mineralisation will make the nitrogen in these crop residues and roots available again for uptake.

A simple waterbalance calculates the soil moistere content and water leaching. In the Netherlands there is a surplus of rainfall in authumn and winter, while crop uptake in those periods is low. Then mineral nitrogen is transported down the soil profile. When the nitrogen gets out of reach of plant roots it is considered lost. The actual nitrogen leaching depends on time, place and quantity of mineral nitrogen in the soil. Also the leaching factor of the soil and the occurence of bypass flow influence how much nitrogen will be lost.

In the topsoil supply of mineral nitrogen by deposition takes place. Yearly deposition can be given and is distributed equal over the year.

Crop nitrogen uptake is calculated from actual or intended crop yield, dry matter distribution and nitrogen contents product, residu and root.

Legume crops do not take up all the required nitrogen from the soil but use gaseous nitrogen from the air which is fixed by symbiontic microorganisms. When the available mineral nitrogen in the soil exceeds a thresshold value, fixation is reduced.

Cultivation has an effect on nitrogen mineralisation. This effect is included in the model by replacing a part of the slowly mineralising old initial organic matter with an equal quantity of faster mineralising organic matter. Comparative research at Westmaas research farm on different cultivation systems gives an indication of the size of the effect on clay soil.


Model overview: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Nitrogen balance

References

Publications


Waterbalance
2 Waterbalance

See also	Symbols	Formulas	Figures	Tables

In NDICEA the soil consists of two layers (see figure 2). In the top layer (hereby called topsoil) tillage, application of organic matter and mineralisation take place. The second layer (hereby called subsoil) is important for storage of water and nutrients. It reaches to where crops can take up water and nutrients. Predefined soil types with their properties can be imported from a standard file.

Figure 2: Schematic representation 2-layer model.

It is assumed that every timestep within each layer complete mixing of soil water takes place.

At the beginning of each timestep the moisture content and matrix suction are calcaluted for both layers. Precipitation, which can be obtained from the nearest weather station, and irrigation are added to the available water of the topsoil. Depending on the pF of each layer, capillary rise can take place into both layers (negative matrixflow).

Plants can take up water from both layers. Which fraction is taken from the topsoil depends on crop rooting depth. Intended crop water uptake is determined by development stage and potential evapotranspiration. Modelled uptake is limited by plant available water and soil pF. Water above field capacity present at the end of every time step percolates to the deeper layer. Water leached from the subsoil is lost from the system. By capillary rise groundwater can enter the system.


Waterbalance: Symbols
Symbols

Waterbalance

Rain = Rainfall [mm/week]

Irri = Irrigation [mm/week]

ByPassFlow = Bypass flow soil layer [mm/week]

DiffFlow = Differential flow from matrix to bypass flow [mm/week]

Upt = Modelled water uptake from soil layer [mm/week]

MatrixFlowIn = Matrix flow into soil layer [mm/week]

MatrixFlowOut = Matrix flow out of soil layer [mm/week]

FlowOut = Total flow out of soil layer [mm/week]


Waterbalance: See also
See also

Introduction

Model overview

Waterbalance

Soil pF-curve

Watertable

Field capacity

Capillary rise

Bypass flow

Crop cover

Evapotranspiration

Rooting depth

Root density

Calculation of waterbalance

Mineralisation

Nitrogen balance

References

Publications


Soil pF curve
2.1 Soil pF curve

See also	Symbols	Formulas	Figures	Tables

For homogeneous dutch soils the relation between moisture content and matrix suction (or pF) can be described by two parameters SMO and GAM (Driessen, 1988).

Formula 1: Moisture content as a function of matrix suction.

  theta = SMO * psi ^ ( ( - GAM * ln ( psi ) ) )

Formula 2: Matrix suction as a function of moisture content.

  psi = e ^ ( SQRT ( 1 / GAM * ln ( SMO / theta ) ) )

Formula 3: Definition of soil pF value.

  pF = log ( psi )

Formula 4: Redefinition of moisture content.

  M = 10 * THL * theta

Figure 3: Calculated pF-curves for some soiltypes.

Some GAM en SMO values for different soil types can be found in Appendix I: Example standard soils (*.SOI). They can be defined for topsoil and subsoil separately and determine the pF-curve for that layer. The pF-curve gives the relation between soil moisture content and soil matrix suction (figure 3). From the pF-curve follows the quantity of plant available soil moisture between field capacity (pF=2.0) and wilting point (pF=4.21). Above wilting point moisture is so tightly bound that plant roots can not take it up anymore. Using the thickness of the layers NDICEA expresses the moisture content of a layer in millimeter water (quantity of water per unit of area).


Soil pF curve: Symbols
Symbols

Soil pF curve

psi = Matrix suction soil layer (cm)

theta = Moisture content soil layer (m3/m3)

SMO = Saturated soil moisture content (m3/m3)

GAM = Coefficient influencing shape of soil pF curve: the higher the value the steeper the change of matrix suction with soil moisture content [/cm2]

M = Moisture content soil layer (mm)


Watertable
2.2 Watertable

See also	Symbols	Formulas	Figures	Tables

To include capillary rise in the model, the water table is introduced as an exogenous variable. It is assumed that the same pattern repeats every year. Two points in a year can be given. A week of maximum and a week of minimum level. These points are then interpolated linear. Also, by giving the nitrogen content at the week of maximum and minimum level, import of nitrogen by capillary rise can be calculated.

Figure 4: Ground water table.

The concentration of mineral nitrogen in the ground water at the weeks of extreme ground water table is expressed in mg/l and is also interpolated linear.

Formula 5: Ground water table.

if WoY < GWTwk1 then

  tmp = (WoY + 52 - GWTwk2) / (GWTwk1 + 52 - GWTwk2)

  GWT = GWT2 + tmp * (GWT1 - GWT2)

  NGW = NGW2 + tmp * (NGW1 - NGW2)

else if WoY <= GWTwk2 then

  tmp = (WoY - GWTwk1) / (GWTwk2 - GWTwk1)

  GWT = GWT1 + tmp * (GWT2 - GWT1)

  NGW = NGW1 + tmp * (NGW2 - NGW1)

else

  tmp = (WoY - GWTwk2) / (GWTwk1 + 52 - GWTwk2)

  GWT = GWT2 + tmp * (GWT1 - GWT2)

  NGW = NGW2 + tmp * (NGW1 - NGW2)

Maximum and minimum watertable levels [cm] must be larger than the depth of the subsoil. If they are not, they will be automatically set 5 cm larger than the depth of the subsoil.


Watertable: Symbols
Symbols

Watertable

GWT = Level of ground water table (cm)

GWT1 = First level of extreme ground water table (cm)

GWT2 = Second level of extreme ground water table (cm)

GWTwk1 = First week of extreme ground water table (week 1-52)

GWTwk2 = Second week of extreme ground water table (week 1-52)

NGW = Nitrogen content ground water [mg/l]

NGW1 = First nitrogen content ground water (mg/l)

NGW2 = Second nitrogen content ground water (mg/l)

WoY = Time variable (week of year 1-52)


Field capacity
2.3 Field capacity

See also	Symbols	Formulas	Figures	Tables

Equilibrium matrix suction for topsoil and subsoil is calculated as the distance of the center of the layer to the watertable. Field capacity is the matrix suction where water starts to percolate. If the distance to the watertable is less then 100 cm fieldcapacity is assumed equal to equilibrium matrix suction else field capacity is assumed at 100 cm (pF=2).

Formula 6: Equilibrium matrix suction topsoil.

  psiGWT[1] = GWT - THL[1] / 2

Formula 7: Equilibrium matrix suction subsoil.

  psiGWT[2] = GWT - THL[1] - THL[2] / 2

Formula 8: Matrix suction at field capacity.

  psiFC = min( psiGWT, 100 )

Formula 9: Moisture content at field capacity.

  MFC = 10 * THL * SMO * psiFC ^ ( - GAM * ln ( psiFC ) )

Using the equilibrium matrix suction, maximum capillary rise, for topsoil and subsoil, can be calculated from watertable for every week.


Field capacity: Symbols
Symbols

Field capacity

SMO = Saturated soil moisture content (cm3/cm3)

GAM = Coefficient influencing shape of soil pF curve: the higher the value the steeper the change of matrix suction with soil moisture content [/cm2]

GWT = Level of ground water table [cm below surface]

THL = Thickness soil layer [cm]

psiGWT = Equilibruim matrix suction = distance of center of layer to watertable [cm]

psiFC = Matrix suction soil layer at field capacity [cm]

MFC = Moisture content soil layer at field capacity [mm]


Capillary rise
2.4 Capillary rise

See also	Symbols	Formulas	Figures	Tables

Using the equilibrium matrix suction, maximum capillary rise, for topsoil and subsoil, is calculated from watertable for every week.

Figure 5: Distance to ground water table and maximum capillary rise for different soil types (Anonymus, 1989).

Maximum capillary rise for the topsoil is calculated from the distance to the subsoil and a virtual watertable at field capacity subsoil.

Formula 10: Maximum capillary rise topsoil.

  CRmax[1] = 7 * e ^ ( ( CRc[1] - THL[1] / 2 - psiFC[2] ) / CRx[1] )

Maximum capillary rise for the subsoil is calculated from the distance to the watertable.

Formula 11: Maximum capillary rise subsoil.

  CRmax[2] = 7 * e ^ ( ( CRc[2] - psiGWT[2] ) / CRx[2] )

The coefficients CRc and CRx for different soil types were determined by applying regression analyses on data from a table containing 'distances between rootzone and soilwater [cm] allowing certain amounts of capillary rise [mm/day] for different soil types' (Anonymus, 1989, p.214). Because this table gives values for capillary rise up to 3 mm a maximum for  CRmax is set at 21 mm/week.

The actual capillary rise depends on the weekly calculated waterbalance.


Capillary rise: Symbols
Symbols

Capillary rise

psiGWT = Equilibruim matrix suction = distance of center of layer to watertable [cm]

psiFC = Matrix suction soil layer at field capacity [cm]

GWT = Level of ground water table [cm below surface]

THL = Thickness soil layer [cm]

CRmax = Maximum capillary rise [mm/week]

CRc = Distance above water table where potential capillary rise is equal to 1 mm/day [cm]

CRx = Distance above CRc where potential capillary rise decreases a factor e [cm]


Bypass flow
2.5 Bypass flow

See also	Symbols	Formulas	Figures	Tables

If the flow intensity at the top of a soil layer exceeds a bypass flow thresshold (FI) bypass flow takes place. A fraction (BPF) of the flow will bypass the layer without mixing. The part entering and mixing with the moisture in the layer is called matrix flow.

Formula 12: Bypassflow topsoil.

  if Rain + Irri > FI[1] then

    ByPassFlow[1] = (Rain + Irri) * BPF[1]

  else

    ByPassFlow[1] = 0

For the subsoil the sum of matrix flow and bypass flow from the topsoil determine if and how much bypass flow takes place. For further calculations DiffFlow[2] is defined as the differential flow between matrix and bypass flow. If bypass flow in the subsoil is less than in the topsoil DiffFlow[2] will be negative (See figure 2).

Formula 13: Differential flow subsoil.

  If MatrixFlowOut[1] + ByPassFlow[1] > FI[2] then

    DiffFlow[2] = (MatrixFlowOut[1] + ByPassFlow[1]) * BPF[2] - ByPassFlow[1]

  else

    DiffFlow[2] = - ByPassFlow[1]

Bypass flow plus matrix flow out of the subsoil form the total flow out of the subsoil (water leaching).


Bypass flow: Symbols
Symbols

Bypass flow

Rain = Rainfall [mm/week]

Irri = Irrigation [mm/week]

FI = Flow Intensity where bypass flow starts [mm/week]

ByPassFlow = Bypass flow soil layer [mm/week]

DiffFlow = Differential flow from matrix to bypass flow [mm/week]

BPF = ByPass Flow factor: fraction bypass flow of total flow [-]

MatrixFlowOut = Matrix flow out of soil layer [mm/week]


Crop cover
2.6 Crop cover

See also	Symbols	Formulas	Figures	Tables

Crop development is described by four points in time: Sowing , Full cover, Ripening and Harvest.

Figure 6: Crop cover at different crop development stages.

The crop cover factor (CC) increases linear from 0 to 1 from sowing to maximum cover, then remains constant until ripening, and then decreases linear again to 0.5 at harvest:

Formula 14: Crop cover factor.

  if (t < Sowing) or (t > Harvest) then

    CC = 0

  else if t < FullCover then

    CC = (t - Sowing) / (FullCover - Sowing)

  else if t < Ripening then

    CC = 1

  else

    CC = 1 - 0.5 * (t - Ripening) / (Harvest - Ripening)


Crop cover: Symbols
Symbols

Crop cover

t = Time variable [weeks]

Sowing = Time of planting or crop emergence [weeks]

FullCover = Time when crop reaches maximum evapotranspiration factor and maximum rooting depth [weeks]

Ripening = Time when ripening starts [weeks]

Harvest = Time of crop harvest [weeks]

CC = Crop cover factor [-]


Evapotranspiration
2.7 Evapotranspiration

See also	Symbols	Formulas	Figures	Tables

Weekly intended water evapotranspiration (UptI [mm/week]) is calculated using crop cover. Bare soil is assumed to have a constant evaporation factor ETbare. Always the highest value of the CC * ETmax and ETbare is taken.

Formula 15: Intended crop evapotranspiration.

  UptI = max(CC * ETmax , ETbare) * ET0

For overlapping crops also the highest of the CC * ETmax is taken. Potential evapotranspiration (ET0 [mm/week]) is taken from the nearest weather station and the maximum crop evapotranspiration factor (ETmax [-]) for example from Hooghart (1987).


Evapotranspiration: Symbols
Symbols

Evapotranspiration

UptI = Intended crop water uptake [mm/week]

CC = Crop cover factor [-]

ETmax = Maximum crop evapotranspiration factor [-]

ETbare = Evaporation factor bare soil [-]

ET0 = Reference crop evapotranspiration [mm/week]


Rooting depth
2.8 Rooting depth

See also	Symbols	Formulas	Figures	Tables

Similar to crop cover, crop rooting depth increases linear from 0 to a maximum rooting depth between week of sowing and week of maximum cover, after that it remains constant.

Formula 16: Crop rooting depth.

  if (t < Sowing) or (t > Harvest) then

    RD = 0

  else if t < FullCover then

    RD = (t - Sowing) / (FullCover - Sowing) * RDmax

  else

    RD = RDmax

Figure 7: Crop rooting depth.


Rooting depth: Symbols
Symbols

Rooting depth

t = Time variable [weeks]

Sowing = Week of planting or crop emergence [-]

FullCover = Week when crop reaches maximum evapotranspiration factor and maximum rooting depth [-]

Ripening = Week when ripening starts [-]

Harvest = Week of crop harvest [-]

RD = Rooting depth [cm]

RDmax = Maximum crop rooting depth [cm]


Root density
2.9 Root density

See also	Symbols	Formulas	Figures	Tables

A linear decrease of root density with depth is assumed. From rooting depth the fraction of total roots in the topsoil is calculated.

Formula 17: Root density.

  if RD < THL[1] then

    RF[1] = 1

  else

    RF[1] = 1 - ((RD - THL[1]) / RD) ^ 2

This fraction is used to calculate the water uptake from topsoil and subsoil. At a rooting depth of 2*THL[1] the fraction is 0.75, at 3*THL[1] 0.56 and at 4*THL[1] 0.44.

In case there is no crop, rooting depth will be 0 and RF[1] will be equal to 1. So evapo(transpi)ration bare soil will be taken from the topsoil.

While rooting depth may be deeper than subsoil, watertable, depth and pF of the subsoil still determine capillary rise into the subsoil, not rooting depth. Though, a dryer subsoil in an earlier stage, by increased water uptake from the subsoil instead of the topsoil, can cause a greater capillary rise into the subsoil and thus more total crop available water.


Root density: Symbols
Symbols

Root density

RD = Rooting depth [cm]

THL = Thickness of soil layer [cm]

RF = Fraction of all roots in soil layer [-]


Calculation of waterbalance
2.10 Calculation of waterbalance

See also	Symbols	Formulas	Figures	Tables

The moisture content at the beginning of every week  is calculated from the moisture content at the previous week.

Formula 18: Moisture content soil layers.

M[t+1] = M[t] + MatrixFlowIn[t] - Upt[t] - MatrixFlowOut[t]

If rainfall plus irrigation exceeds the bypass flow thresshold (FI), a part will bypass the topsoil.

Formula 19: Matrixflow into topsoil.

MatrixFlowIn[1] = Rain + Irri - ByPassFlow[1]

The same goes for the subsoil: if the sum of matrix flow and bypass flow from the topsoil exceeds the bypass flow thresshold of the subsoil, a part (see eq. 10) will bypass the subsoil. Remember that ByPassFlow[2] is defined as the differential flow between matrix and bypass flow.

Formula 20: Matrixflow into subsoil.

MatrixFlowIn[2] = MatrixFlowOut[1] - DiffFlow[2]

If moisture content at the beginning of the timestep is less than field capacity capillary rise can take place. The coefficients CRc and CRx that are used to calculate CRmax (see formula 10 and 11) are based on a table for a rootzone that has dried to pF 2.4. Assuming no capillary rise would take place when the pF of the rootzone was equal to 2.0 a required pF difference of 0.4 is assumed nescessary to reach ETmax. When pF topsoil is less than pF subsoil, no capillary rise takes place.

Formula 21: Capillary rise topsoil.

CR[1] = CRmax[1] * max ( min ( (pF[1] - pF[2]) / 0.4 , 1 ) , 0 )

Formula 22: Capillary rise subsoil.

CR[2] = CRmax[2] * max ( min ( (pF[2] - pFpsiGWT) / 0.4 , 1 ) , 0 )

Crop water uptake is first calculated for the topsoil, then for the subsoil. Uptake from each layer can never exceed available water above wilting point (including the current weeks matrix flow and capillary rise into the layer) and water uptake is reduced by a water uptake factor depending on soil pF.

Figure 8: Water uptake factor at different soil pF.

When the soil pF at the beginning of a timestep rises above 2.7 the water uptake from the layer is reduced. The water uptake factor then decreases linear from 1 to zero at wilting point (pF=4.21).

Formula 23: Water uptake factor.

WUF = max ( min ( ( 4.21 - pF ) / ( 4.21 - 2.7 ) , 1 ) , 0 )

As long as the pF of the subsoil does not exceed 2.7, uptake from topsoil is limited by the water uptake factor and by the rootfraction in the topsoil. When the pF of the subsoil increases above 2.7 the model tries to take up all required water (UptI) from the topsoil, independant of rooting depth.

Formula 24: Water uptake topsoil.

if pF[2] < 2.7 then Upt[1] = WUF[1] * UptI * RF[1]

else Upt[1] = WUF[1] * UptI

After calculating the uptake from the topsoil the model will try to take up the remaining water requirement from the subsoil, but only if rooting depth is deeper than the thickness of the topsoil.

Formula 25: Water uptake subsoil.

if RF[1] = 1 then Upt[2] = 0

else Upt[2] = WUF[2] * (UptI - Upt[1])

For both topsoil and subsoil the model does not allow moisture content to decrease below wilting point.

Formula 26: Limitation of water uptake by wilting point.

Upt = min ( Upt , M + MatrixFlowIn + CR - MWP )

MatrixFlowOut is the water flow at the bottom of the layer including capillary rise. Water above field capacity at the end of the timestep will flow out. An extra limitation is added to avoid moisture content to exceed field capacity due to negative matrixflow or capillary rise (CR).

Formula 27: Matrixflow out of soil layer.

tmp = M + MatrixFlowIn + CR - Upt - MFC

if tmp > 0 then

  MatrixFlowOut = tmp - CR

else if tmp < - CR then

  MatrixFlowOut = - CR

else

  MatrixFlowOut = tmp


Calculation of waterbalance: Symbols
Symbols

Calculation of waterbalance

t = Time variable [weeks]

M = Moisture content soil layer (mm)

MatrixFlowIn = Matrix flow into soil layer [mm/week]

Upt = Modelled water uptake from soil layer [mm/week]

MatrixFlowOut = Matrix flow out of soil layer [mm/week]

Rain = Rainfall [mm/week]

Irri = Irrigation [mm/week]

ByPassFlow = Bypass flow soil layer [mm/week]

DiffFlow = Differential flow from matrix to bypass flow [mm/week]

CR = Capillary rise into soil layer [mm/week]

CRmax = Maximum capillary rise into layer [mm/week]

pF = pF soil layer [-]

pFGWT = pF soil layer at equilibrium matrix suction [-]

WUF = Water uptake reduction factor [-]

RF = Fraction of all roots in soil layer [-]

UptI = Intended water uptake [mm/week]

MWP = Moisture content soil layer at wilting point [mm]

MFC = Moisture content soil layer at field capacity [mm]

tmp = temporary variable


Mineralisation
3 Mineralisation

See also	Symbols	Formulas	Figures	Tables

Janssen's formula (1984) is based on empirical data from Kortleven (1963), who studied the yearly decomposition of applied organic matter in bare soils. Kortleven introduced the term 'humification coefficient' as the fraction remaining one year after application of organic matter to the soil. Humification coefficients were determined on a year basis on bare fields under Dutch circumstances. The remaining quantity of organic carbon after one year for each application can be calculated using the humification coefficient h.

Formula 28: Definition of effective organic matter.

C[y=1 year] = h * C[y=0 years]

When C represents the total quantity of organic carbon in the soil, the rate of decay can be described as:

Formula 29: Exponential decay with constant k.

dC / dy = - k * C

According to Janssen the decayrate k for every organic matter applied to the soil is variable. With time, k decreases.

Formula 30: Variable decayrate k according to Janssen.

k = 2.82 * (a + y) ^ - 1.6

The coefficients of this formula are based on empirical data. This formula is only valid for inital age and time expressed in years.The decay of every organic matter thus can be characterised with a single parameter, the apparent initial age a. Table 1 gives some values of a for different types of organic matter.

Table 1: Humificationcoëfficiënts and apparent initial age for some types of organic matter (Janssen, 1988)

Organic Matter	h	a

green material	0.45	0.99

straw	0.57	1.41

bedding material	0.71	2.28

stable manure	0.73	2.45

fir needles	0.80	3.36

saw dust	0.82	3.69

peat 1	0.83	3.95

peat 2	0.88	5.47

peat 3	0.92	7.87

peat 4	0.96	13.62

When C[y=0] represents the initial applied quantity of organic matter, the integrated form of Janssen's formula looks as follows:

Formula 31: Janssen's formula.

C[y] = C[y=0] * exp( 4.7 * ( (a + y) ^ (- 0.6) - a ^ (- 0.6) ) )

Figure 9: Decomposition of 100 ton organic matter with different apparent initial age.

Mineralisation of organic matter already present in the soil, or initial organic matter, can be described with the same formula. When mineralisation from initial organic matter is equal to 2%, the humification coëfficient would be 0.98 and the apparent initial age about 24 years.

From formula 28 and 31 follows a relation between h and a.

Formula 32: Relation between humification coefficient and apparent initial age.

h = C[y=1] / C[y=0] = exp( 4.7 * ( (a + 1) ^ (- 0.6) - a ^ (- 0.6) ) )

With this formula the initial age a can be derived from the humification coëfficiënt h iteratively.

Figure 10: Relation between humification coefficient and apparent initial age.


Mineralisation: Symbols
Symbols

Mineralisation

y = Time variable [years]

C = Amount of organic carbon [kg]

h = Humification coëfficient [-]

k = Decay rate [-]

a = Initial apparent age [years]


Mineralisation: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Rate of aging

Temperature correction factor

Moisture correction factor

pH correction factor

Texture correction factor

Cultivation effect

From carbon to nitrogen mineralisation

Nitrogen balance

References

Publications


Rate of aging
3.1 Rate of aging

See also	Symbols	Formulas	Figures	Tables

Janssen's formula has been derived from yearly data on bare, and permanently moist soil in the Netherlands. To describe mineralisation on a cropped soil, within the year, under varying environment circumstances, correction factors have been added for temperature, soil moisture, soil texture and soil pH. Though interaction, for example between temperature and moisture (Cassman en Munns, 1980) is possible, it is assumed that all the correction factors independantly influence mineralisation.

From formula 29 and 30 follows:

Formula 33: Differential form of Janssen's formula.

dC / dy = - 2.82 * (a + y) ^ (- 1.6) * C

When a is called 'initial apparent age', a+y can be called 'apparent age' or 'Age'. Age here increases linear with time.

To refine the procedure a correction factor f is introduced, including a correction for temperature, moisture, texture and pH.

Formula 34: Overall correction factor f for mineralisation rate.

f = fT * fTheta * fText * fpH

This correction factor affects the 'aging' of the organic matter and can also be called the 'rate of aging'.

Formula 35: Definition rate of aging.

f = dAge / dy

For a rate of aging that is not constant formula 33 is rewritten.

Formula 36: Introduction of apparent age in Janssen's formula.

dC / dAge = - 2.82 * Age ^ (- 1.6) * C

Now when formula 35 is substituted in formula 36 the correction factor f appears in Janssen's formula.

Formula 37: Refined differential form of Janssen's formula.

dC / dy = - 2.82 * Age ^ (- 1.6) * C * f

While Janssen's formula describes carbon (C) mineralisation on a year basis, NDICEA directly calculates organic matter (OM) mineralisation on a weekly basis. Assuming C = 0.58 * OM formula 37 can be rewritten.

Formula 38: Organic matter mineralisation on yearly basis.

dOM / dy = - 2.82 * Age ^ (- 1.6) * OM * f

Where dy and Age are expressed in years, f is dimensionless and the dimension of the experimental factor 2.82 is [year^0.6]. To calculate weekly mineralisation, dy expressed in years is replaced by dt expressed in weeks:

Formula 39: From yearly to weekly time scale.

dt = dy * 52

Substituting formula 39 in formula 38 gives:

Formula 40: Organic matter mineralisation on weekly basis.

dOM / dt = (- 2.82 * Age ^ (- 1.6) * OM * f) / 52

To calculate Age (in years) formula 39 can be substituted in formula 35:

Formula 41: Calculating apparent age.

dAge = (f * dt) / 52 or Age = integral(f * dt) / 52

At the moment an organic matter is applied (t=0) Age is equal to initial age a.


Rate of aging: Symbols
Symbols

Rate of aging

y = Time variable [years]

t = Time variable [weeks]

C = Amount of organic carbon [kg]

a = Initial apparent age [years]

f = Overall correction factor = rate of aging [-]

fT = Temperature correction factor [-]

fTheta = Moisture correction factor [-]

fText = Texture correction factor [-]

fpH = pH correction factor [-]

Age = Apparent age [years]

OM = Amount of organic matter [kg]


Temperature correction factor
3.2 Temperature correction factor

See also	Symbols	Formulas	Figures	Tables

Assuming mineralisation is mainly a biological proces, for a quantitative description of the effect of temperature on mineralisation a Q9-equation could be used (Janssen, 1986) or the theoretical approach of Arrhenius (Tate, 1987).

Formula 42: Q9 temperature correction factor.

fTQ9 = 2 ^ ( (T - Tref) / 9 )

Formula 43: Arrhenius temperature correction factor.

fTArrh = exp ^ (- am / R * ( 1 / TK - 1 / TKref ) )

Both the Q9-relation and the Arrhenius equation suggest continued mineralisation at and below 0 oC. At 0 oC the rate of mineralisation would be still 50% of the rate at 9 oC. This may be an overestimation at low temperatures. Little is known about the rate of mineralisation at low temperatures. Bunnel et al (1977) for example, report micro organism activity below 0 oC.

"Results of field trials conducted in England and Nigeria (Jenkinson, 1977; Jenkinson and Ayanaba, 1977) and Australia (Ladd et al., 1981) indicate that the relative mineralization rate of common plant materials was doubled per 9 oC rise in the mean annual temperature. In other words, one year of mineralisation at 27 oC (in Nigeria) was equivalent to two years of mineralisation at 18 oC (in Australia), or to four years of mineralisation at 9 oC (in England). Hence by changing the time scale, it is possible to incorporate the effect of temperature in the equations in a simple way."  (Yang, 1996, p.41)

Based on literature research Yang formulates the following temperature correction factor:

Formula 44: Yang's temperature correction factor.

if T <= -1 then fTYang = 0

else if T <= 9 then fTYang = 0.1 * (T + 1)

else if T <= 27 then fTYang = 2 ^ ( (T - 9) / 9 )

else fTYang = 4

Since initial ages are based on yearly mineralisation under Dutch circumstances a correction factor is applied that matches the weekly temperature factor to the decomposition on a year-basis according to Kortleven, using weather data for an average dutch year. These extra correction factors used are 0.81 for fTQ9, 0.83 for fTArrh and 0.88 for fTYang.

Formula 45: NDICEA temperature correction factor.

fT = 0.88 * fTYang

Figure 11: Comparison of temperature correction factors.

Figure 11 shows that the Q9, Arrhenius and Yang approaches show a substantial difference at low temperatures.


Temperature correction factor: Symbols
Symbols

Temperature correction factor

T = Temperature [oC]

Tref = Reference temperature [oC]

TK = Temperature [Kelvin]

TKref = Reference temperature [Kelvin]

am = Molar activation energie = 47619 [J/mol]

R = Gas constante = 8.314 [J/mol/K]

fTQ9 = Q9 temperature correction factor [-]

fTArrh = Arrhenius temperature correction factor [-]

fTYang = Yang's temperature correction factor [-]

fT = Temperature correction factor [-]


Moisture correction factor
3.3 Moisture correction factor

See also	Symbols	Formulas	Figures	Tables

Huet (1983) gives a summary of several relations in literature for the moisture correction factor for mineralisation rate. The differences between those relations often concern the pF borders.

In NDICEA the moisture correction factor is calculated according to Rijtema (1980): a linear decrease to zero between pF 2.7 and pF 4.21 (figure 12).

Formula 46: Moisture correction factor.

if pF < 2.7 then fTheta = 1

else if pF < 4.21 then fTheta = (4.21 - pF) / (4.21 - 2.7)

else fTheta = 0

Figure 12: Moisture correction factor.


Moisture correction factor: Symbols
Symbols

Moisture correction factor

pF = pF value soil layer [-]

fTheta = Moisture correction factor [-]


pH correction factor
3.4 pH correction factor

See also	Symbols	Formulas	Figures	Tables

In acid circumstances mineralisation of organic matter can be practically reduced to zero. In Bath et al (1980) it is assumed that above pH 4.5 no reduction of mineralisation occurs. Below pH 3.5 mineralisation would completely stop. Rijtema et al.(1991) gives a traject from pH 6 tot pH 4. In normal agricultural practice pH correction for mineralisation is hardly necessary, because soil pH would be improved. For those cases where pH may play an important role a pH correction factor is included: somewhere between the two ranges mentioned with a smooth transition.

Formula 47: pH correction factor.

fpH = 1 / (1 + exp (- 1.5 * (pH - 4) ) )

Figure 13: Correction factor mineralisation by soil pH.


pH correction factor: Symbols
Symbols

pH correction factor

fpH = pH correction factor [-]

pH = Acid value soil layer [-]


Texture correction factor
3.5 Texture correction factor

See also	Symbols	Formulas	Figures	Tables

Mineralisation rate depends on soil texture. Long term experiments have shown that the humus content that can be reached on silty soil is about 1.25 x higher than on sandy soil. The humus content that can be reached on a clay soil is about 1.5 x higher compared to sandy soil.

The texture correction factor fText is included in the overall correction factor for mineralisation rate, f, or rate of aging. Default values for some standard soil types can be found in Appendix 1. Sandy soil has been assigned a default value 1, silty clay 0.67 (=1/1.5) and the other soils were estimated in between based on their texture.


Cultivation effect
3.6 Cultivation effect

See also	Symbols	Formulas	Figures	Tables

Quantification of the effect of cultivation on mineralisation is difficult because it seems to depend on so many complex factors like texture and soil condition during and after the cultivation, influenced by the weather, depth and type of cultivation. It is not yet clear what the origin of the effect is. Probably organic matter is gradually protected from decomposition by the formation of a more resistent skin and enclosure by soil particles. By cultivation, but also by drought and freezing a part of this protected organic matter can be freed (Haynes, 1986). Cultivation effects are included in NDICEA in a simple way by taking a part of the old organic matter and applying it again with a lower apparent initial age. The amount can be estimated from crop rotation research with and without tillage (Titulaer and Boone, 1984; Bakermans and De Wit, 1970).

During eight years from 1972-1979 the organic matter increase in the top 20 cm was 500 kg/ha/year. With reduced tillage this was 2000 kg/ha/year and with minimum tillage 3100 kg/ha/year. From the difference in increase of organic matter over this period the yearly mineralisation due to cultivations can be estimated to 1500 kg/ha/year. Other experiments give a less clear cultivation effect (Bakermans & de Wit, 1970). For example ploughing on a clay soil could give 450 kg old organic matter an apparent initial age of 2.45 year. The choice of this quantity and initial age is arbitrary and up to the user of the model.


From carbon to nitrogen mineralisation
3.7 From carbon to nitrogen mineralisation

See also	Symbols	Formulas	Figures	Tables

Figure 14: Flowdiagram from C to N mineralisation.

The upper part of figure 14 schematically shows the mineralisation of carbon. C represents the varying quantity of organic carbon in the substrate over time. TC and AC are rates at which this quantity changes over time. At the moment of application C is equal to the applied quantity of organic carbon C[t=0]. But as mineralisation proceeds the remaining substrate wil contain less original organic carbon and more in the form of biomass (bacteria, fungi etc), decay- and conversion products. The organic carbon is used by micro-organisms as a source of energy and building material. The rate of consumption of organic carbon is indicated with TC (turnover). The assimilation rate AC indicates which part of this is used again as organic building material, with or without modification.

Different micro organisms can have a different ratio between assimilation and dissimilation of organic matter: ADmicro (Table 2).

Table 2: Average C/N and A/D quotient for some groups of micro-organisms (Hendriks,1992)

Organism	CNmicro	ADmicro

bacteria	5	0.43

actinomycetes	5	0.5

fungi	10	0.5

Dissimilated organic carbon is burnt to CO2 and H2O. Janssen's formula describes this dissimilation DC of organic carbon. Knowing DC and ADmicro, the assimilation AC and turnover TC of organic carbon can be calculated.

Formula 48: Carbon assimilation by micro organisms.

AC = ADmicro * DC

Formula 49: Carbon turnover by micro organisms.

TC = (1 + ADmicro ) * DC

The lower part of figure 14 schematically shows the dissimilation of nitrogen DN. Assimilation of nitrogen AN follows from the assimilation of carbon AC and the carbon to nitrogen ratio of the microorganisms (CNmicro).

Formula 50: Nitrogen assimilation by micro organisms.

AN = 1 / CNmicro * AC

The turnover of nitrogen (TN) is related to the turnover of organic carbon (TC) and the current carbon to nitrogen ratio of the substrate.

Formula 51: Nitrogen turnover by micro organisms.

TN = 1 / CN[t] * TC

Formula 52: Current CN ratio organic matter.

CN[t] = C[t] / N[t]

While CN[t] changes in time, CNmicro is assumed constant. The difference between turnover and assimilation of nitrogen gives the net mineralisation of nitrogen DN.

Formula 53: From carbon to nitrogen mineralisation.

DN = TN - AN = ( (1 + ADmicro ) / CN[t] - ADmicro / CNmicro ) * DC

Substituting DN=dON/dt , DC=dC/dt and assuming C = 0.58 * OM formula 53 can be rewritten for organic matter instead of organic carbon.

Formula 54: From organic matter to nitrogen mineralisation.

dON / dt = ( (1 + ADmicro) / (OM[t] / ON[t]) - ADmicro / (CNmicro / 0.58) ) * dOM / dt

Figure 15: N-mineralisation of 100 ton organic matter with an initial age of 2.45 at different organic N content.


From carbon to nitrogen mineralisation: Symbols
Symbols

From carbon to nitrogen mineralisation

ADmicro = Assimilation to dissimilation ratio micro organisms [-]

CNmicro = Carbon to nitrogen ratio micro organisms [-]

C = Amount of organic carbon [kg]

AC = Assimilation of carbon [kg/week]

DC = Dissimilation of carbon [kg/week]

TC = Turnover of carbon [kg/week]

ON = Amount of organic nitrogen [kg]

AN = Assimilation of nitrogen [kg/week]

DN = Dissimilation of nitrogen [kg/week]

TN = Turnover of nitrogen [kg/week]

t = Time variable [weeks]

CN = Carbon to nitrogen ratio organic matter [-]

OM = Amount of organic matter [kg]


Nitrogen balance
4 Nitrogen balance

See also	Symbols	Formulas	Figures	Tables

A nitrogen balance for the mineral nitrogen in topsoil and subsoil can be made every timestep using deposition, irrigation, matrix flow into, bypass flow, fixation and the calculated mineralisation of all preceding applications (initial organic matter, crop residues, manure) as inputs. Plant uptake, denitrification and matrix flow out of the layer are outputs. Fixation is accounted for in plant uptake. Capillary rise is included in matrixflow at the bottom of the layer.

Formula 55: Nitrogen balance.

N[t+1] = N[t] + NMatrixFlowIn[t] + NMin[t] - NDen[t] - NUpt[t] - NMatrixFlowOut[t]

Nitrogen deposition and irrigation are added to the flow into the topsoil. Nitrogen bypassflow in the topsoil is subtracted.

Formula 56: Nitrogen matrixflow into topsoil.

NMatrixFlowIn[1] = NDep + NIrri - NBypassFlow[1]

The nitrogen matrixflow out of the topsoil is added to the flow into the subsoil, the differential nitrogen flow subtracted.

Formula 57: Nitrogen matrixflow into subsoil.

NMatrixFlowIn[2] = NMatrixFlowOut[1] - NDiffFlow[2]

Losses by volatilisation are not modelled. Volatilisation from the soil is assumed of little importance. To account for volatilisation from applied manure it could be subtracted in advance.


Nitrogen balance: Symbols
Symbols

Nitrogen balance

t = Time variable [weeks]

N = Nitrogen content soil layer [kg N/ha]

NDep = Nitrogen deposition [kg N/ha/week]

NIrri = Nitrogen irrigation [kg N/ha/week]

NMin = Nitrogen mineralisation soil layer [kg N/ha/week]

NDen = Denitrification in soil layer [kg N/ha/week]

NUpt = Modelled nitrogen uptake from soil layer [kg N/ha/week]

NMatrixFlowIn = Nitrogen matrix flow into soil layer [kg N/ha/week]

NMatrixFlowOut = Nitrogen matrix flow out of soil layer [kg N/ha/week]

NByPassFlow = Nitrogen bypass flow at soil layer [kg N/ha/week]

NDiffFlow = Differential flow of nitrogen from matrix to bypass flow [kg N/ha/week]


Nitrogen balance: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Nitrogen balance

Nitrogen deposition

Nitrogen irrigation

Denitrification

Nitrogen uptake

Nitrogen fixation

Nitrogen matrixflow

Nitrogen bypassflow

References

Publications


Nitrogen deposition
4.1 Nitrogen deposition

See also	Symbols	Formulas	Figures	Tables

Nitrogen deposition is an input of mineral nitrogen to the topsoil. Deposition differs for every region. RIVM (Anonymus,1990) gives for 1989 for the area around Wageningen 49 kg N/ha/year. In NDICEA the yearly deposition is divided equally over the year. It can be divided manually by adding it as irrigation.

Formula 58: Deposition per week.

NDep[week] = NDep[year] /  52


Nitrogen deposition: Symbols
Symbols

Nitrogen deposition

NDep[week] = Nitrogen deposition [kg N/ha/week]

NDep[year] = Nitrogen deposition [kg N/ha/year]


Nitrogen irrigation
4.2 Nitrogen irrigation

See also	Symbols	Formulas	Figures	Tables

Weekly irrigation (NIrri) of nitrogen can be entered in an irrigation file, together with water irrigation (Irri), and will be added to the topsoil.


Nitrogen irrigation: Symbols
Symbols

Nitrogen irrigation

Irri = Irrigation [mm/week]

NIrri = Nitrogen irrigation [kg N/ha/week]


Denitrification
4.3 Denitrification

See also	Symbols	Formulas	Figures	Tables

Calculation of denitrification is based on Bradbury et al (1993) with some modifications. It is proportional to 'organic matter mineralisation',  'mineral N above a thresshold' and 'moisture content above wilting point'.

Formula 59: Denitrification.

NDen = DNF / 1000 * dOM / dt * (N - DN0) * (M - MWP) / (MFC - MWP)

For the topsoil dOM/dt represents the mineralisation of all initial and added organic matters, for the subsoil dOM/dt concerns only the mineralisation of one initial organic matter.


Denitrification: Symbols
Symbols

Denitrification

NDen = Denitrification in soil layer [kg N/ha/week]

DNF = Denitrification factor soil layer [kg/1000 kg OM/kg N]

OM = Organic matter in soil layer [kg]

t = Time variable [weeks]

N = Mineral nitrogen content of soil layer [kg N/ha]

DN0 = Denitrification thresshold [kg N/ha]

M = Moisture content soil layer [mm]

MWP = Moisture content soil layer at wilting point [mm]

MFC = moisture content soil layer at field capacity [mm]


Nitrogen uptake
4.4 Nitrogen uptake

See also	Symbols	Formulas	Figures	Tables

Total crop nitrogen uptake (NUptCrop) is calculated from actual or intended product yield, dry matter content product (DMcProd), dry matter distribution over product, residue and root (fProd, fResi, fRoot), and nitrogen content product, residue and root (NcProd, NcResi, NcRoot).

Formula 60: Total crop nitrogen uptake.

NUptCrop = Prod * DMcProd / fProd * (fProd * NcProd + fResi * NcResi + fRoot * NcRoot)

If important, a quantity of seed or planting material can be supplied. The nitrogen in it will be subtracted from the crop uptake.

Formula 61: Total crop nitrogen uptake minus seed.

NUptCrop = NUptCrop - Seed * DMcSeed * NcSeed

Distribution of the intended nitrogen uptake of a crop over its growing period is calculated after the water balance has been calculated. Nitrogen uptake will be reduced by dryness if water uptake is less than a fraction MWU of the intended water uptake. Using the weekly fraction 'uptake/ intended uptake' a weighing factor for weekly intended crop nitrogen uptake is determined.

Formula 62: Weighing factor for nitrogen uptake.

if (Upt[1] + Upt[2]) / UptI < MWU then

  fNUpt = (Upt[1] + Upt[2]) / (UptI * MWU) * CC * ETmax * ET0

else

  fNUpt = CC * ETmax * ET0

Then the weekly intended crop nitrogen uptake is calculated using total intended crop nitrogen uptake, the weekly weighing factors and the summed weighing factors over the crop period. Nitrogen uptake for overlapping crops is assumed additive. Intended nitrogen fixation is subtracted from intended nitrogen uptake.

Formula 63: Intended nitrogen uptake.

NUptI = NUptCrop * fNUpt / integral(fNUpt) - NFixI

The nitrogen uptake from topsoil and subsoil is assumed proportional to water uptake and mineral nitrogen concentration.

Formula 64: Nitrogen uptake from topsoil.

NUpt[1] = p[1] * Upt[1] * N[1] / M[1]

Formula 65: Nitrogen uptake from subsoil.

NUpt[2] = p[2] * Upt[2] * N[2] / M[2]

The proportionality factor p can be different for every timestep but is assumed equal for both layers.

Formula 66: Proportionality factor nitrogen uptake from topsoil and subsoil.

p[1] = p[2] = p

The total uptake from both layers:

Formula 67: Intended nitrogen uptake A.

NUptI = NUpt[1] + NUpt[2]

Now formula 66 can be substituted into 64 and 65. Then 64 and 65 can be substituted into 67, leading to 68.

Formula 68: Intended nitrogen uptake B.

NUptI = p * ( Upt[1] * N[1] / M[1] + Upt[2] * N[2] / M[2] )

Solving k from equation 67 and inserting it in equation 63 and 64 gives the formulas for the modelled N uptake from the topsoil and the subsoil.

Formula 69: Modelled nitrogen uptake from the topsoil.

NUpt[1] = NUptI / (1 + (Upt[2] / Upt[1]) * (N[2] / N[1]) * (M[1] / M[2]) )

Formula 70: Modelled nitrogen uptake from the subsoil.

NUpt[2] = NUptI - NUpt[1]

The nitrogen uptake from each layer can not exceed the available mineral nitrogen in that layer.

Within each timestep first matrix flow of nitrogen into the layer is calculated. Then nitrogen mineralisation is added and denitrification and nitrogen uptake are subtracted. Finally matrix flow of nitrogen out of the layer (or capillary rise) is calculated.


Nitrogen uptake: Symbols
Symbols

Nitrogen uptake

NUptCrop = Total crop nitrogen uptake [kg N/ha]

Prod = Quantity of crop product yield [kg/ha]

Resi = Quantity of crop residues [kg/ha]

Root = Quantity of crop roots [kg/ha]

Seed = Applied seed quantity or planting material [kg/ha]

DMcProd = Dry matter content product [kg/kg]

DMcSeed = Dry matter content seed [kg/kg]

fProd = Fraction product | residue | root of total dry matter [-]

fResi = Fraction residues of total dry matter [-]

fRoot = Fraction roots of total dry matter [-]

NcProd = Nitrogen content in dry matter product [kg/kg]

NcResi = Nitrogen content in dry matter residues [kg/kg]

NcRoot = Nitrogen content in dry matter roots [kg/kg]

NcSeed = Nitrogen content in dry matter seed [kg/kg]

Upt = Modelled water uptake from soil layer [mm/week]

UptI = Intended crop water uptake [mm/week]

MWU = Minimum Water Uptake fraction for maximum nitrogen uptake [-]

fNUPT = Weighing factor for weekly intended crop nitrogen uptake and fixation [-]

CC = Crop cover factor [-]

ETmax = Maximum crop evapotranspiration factor [-]

ET0 = Reference crop evapotranspiration [mm/week]

p = Proportionality between water uptake, nitrogen concentration and N-uptake [-]

NUptI = Intended crop nitrogen uptake [kg N/ha/week]

NUpt = Modelled nitrogen uptake from soil layer [kg N/ha/week]

NFixI = Intended crop nitrogen fixation [kg N/ha/week]

N = Mineral nitrogen content soil layer [kg N/ha]

M = Moisture content soil layer [mm]


Nitrogen fixation
4.5 Nitrogen fixation

See also	Symbols	Formulas	Figures	Tables

Symbiontic fixation can take place in grass-clover and leguminous crops. N-fixation of grass-clover could be estimated from dry matter yield and clover percentage (Ennik, 1982). In NDICEA fixation is calculated using the crops total intended fixation NFixI, and a thresshold of mineral nitrogen in the topsoil above which fixation is reduced. It is assumed that nitrogen fixing crops like grass-clover and legumes do not start fixing nitrogen until it becomes harder for them to take it up from the soil (Van Mil, 1981).

The distribution of the intended nitrogen fixation over the growing period is calculated exactly like the intended nitrogen uptake.

Formula 71: Intended weekly nitrogen fixation.

NFixI = NFixCrop * fNUpt / integral(fNUpt)

Intended nitrogen fixation for overlapping crops is assumed additive and intended nitrogen fixation can never exceed intended nitrogen uptake.

Above the thresshold NFix0 the weekly intended fixation is reduced depending on the mineral nitrogen content in the topsoil N[1].

Formula 72: Reduced intended nitrogen fixation.

NFixI = NFixI * max ( min ( 2 - N[1] / NFix0 , 1 ) , 0 )


Nitrogen fixation: Symbols
Symbols

Nitrogen fixation

NFixI = Intended crop nitrogen fixation [kg N/ha/week]

NFixCrop = Potential crop nitrogen fixation [kg N/ha]

fNUPT = Weighing factor for weekly intended crop nitrogen uptake and fixation [-]

N = Mineral nitrogen content soil layer [kg N/ha]

NFix0 = Nitrogen fixation thresshold [kg N/ha in topsoil]


Nitrogen matrixflow
4.6 Nitrogen matrixflow

See also	Symbols	Formulas	Figures	Tables

Nitrogen matrix flow is proportionate to matrix water flow and the mineral nitrogen concentration in the layer. The water content (M) and the nitrogen content (N) for topsoil and subsoil are calculated at the beginning of each timestep.

Formula 73: Nitrogen matrix flow out of soil layer.

NMatrixFlowOut = MatrixFlowOut * N / M * NLF

Water transport is not homogeneous through the soil. A part of the water will follow larger pores and cracks while mineral nitrogen is also present in smaller pores, especially nitrogen gradually mineralised from soil organic matter. Also by reduced nitrification in winter and adsorption of the ammonium, a part of the mineral nitrogen can escape from waterflow. To account for this phenomena of preferent waterflows and adsorption a nitrogen leaching factor NLF for every layer is introduced. It is difficult to find standard values for NLF in literature; the phenomena is still in research (Bouma & Dekker, 1978; Bronswijk et al, 1990). The standard soil file contains estimated values.

In case of capillary rise (MatrixFlowOut < 0) no leaching factor is used. Then for the topsoil the nitrogen concentration from the subsoil and for the subsoil the nitrogen concentration of the groundwater (NGW) is used.

Formula 74: Nitrogen matrix flow out of topsoil in case of capillary rise.

NMatrixFlowOut[1] = MatrixFlowOut[1] * N[2] / M[2]

Formula 75: Nitrogen matrix flow out of subsoil in case of capillary rise.

NMatrixFlowOut[2]=MatrixFlowOut[2] * NGW / 100


Nitrogen matrixflow: Symbols
Symbols

Nitrogen matrixflow

NMatrixFlowOut = Nitrogen matrix flow out of soil layer [kg N/ha/week]

MatrixFlowOut = Matrix flow of water out of soil layer [mm/week]

N = Mineral nitrogen content soil layer [kg N/ha]

M = Moisture content soil layer [mm]

NGW = Nitrogen content ground water [mg/l]


Nitrogen bypassflow
4.7 Nitrogen bypassflow

See also	Symbols	Formulas	Figures	Tables

The water bypass flow calculated in the water balance is used to determine the nitrogen bypass flow. Nitrogen in deposition and irrigation can go to the bypass flow of the topsoil.

Formula 76: Nitrogen bypass flow topsoil.

NByPassFlow[1] = (NDep + NIrri) * ByPassFlow[1] / (MatrixFlowIn[1] + ByPassFlow[1])

DiffFlow[2] is defined as the differential water flow between matrix flow and bypass flow. If DiffFlow[2] is positive, bypass flow in the subsoil is larger than in the topsoil. Nitrogen from the matrix flow out of the topsoil will go to the bypass flow.

Formula 77: Differential nitrogen flow if differential water flow > 0.

NDiffFlow[2] = NMatrixFlowOut[1] * DiffFlow[2] / MatrixFlowOut[1]

If differential waterflow is negative, bypass flow in the subsoil is smaller than in the topsoil. Nitrogen from ByPassFlow[1] will move to the matrixflow of the subsoil.

Formula 78: Differential nitrogen flow if differential water flow < 0.

NDiffFlow[2] = NByPassFlow[1] * DiffFlow[2] / ByPassFlow[1]


Nitrogen bypassflow: Symbols
Symbols

Nitrogen bypassflow

NByPassFlow = Nitrogen bypass flow at soil layer [kg N/ha/week]

NDep = Nitrogen deposition [kg N/ha/week]

NIrri = Nitrogen irrigation [kg N/ha/week]

ByPassFlow = Bypass flow of water at soil layer [mm/week]

MatrixFlowIn = Matrix flow of water into soil layer [mm/week]

NDiffFlow = Differential flow of nitrogen from matrix to bypass flow [kg N/ha/week]

NMatrixFlowOut = Nitrogen matrix flow out of soil layer [kg N/ha/week]

DiffFlow = Differential flow from matrix to bypass flow [mm/week]

MatrixFlowOut = Matrix flow of water out of soil layer [mm/week]


References

See also	Symbols	Formulas	Figures	Tables

Anonymus, 1989. Handboek voor de akkerbouw en de groenteteelt in de vollegrond 1989. Publicatie nr 47. Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond, Lelystad. p.214.

Anonymus, 1990. Luchtkwaliteit. Jaarverslag 1989. Rapport 222101006. RIVM, Bilthoven.

Bakermans W.A.P. and De Wit C.T., 1970. Crop husbandry on naturally compacted soils. Neth. J. Agric. Sci., 18, 225-246.

Bath K.K.S., Flowers T.H. and O'Callaghan J.R., 1980. A model for the simulation of the fate of nitrogen in farm wastes on land application. Journal of Agricultural Science, 94,1:183-193.

Bouma J. and Dekker L.W., 1978. A case study on infiltration into dry clay soil, I. Morphological observations. Geoderma, 20, 27-40.

Bradbury N.J., Whitmore A.P., Hart P.B.S. and Jenkinson D.S., 1993. Modelling the fate of nitrogen in crop and soil in the years following application of 15N-labelled fertilizer to winter wheat. Journal of Agricultural Science, 121, 363-379.

Bronswijk J.J.B., Dekkers L.W. and Ritsema C.J., 1990. Preferent transport van water en opgeloste stoffen in de Nederlandse bodem: meer regel dan uitzondering, H2O, 22, 594-597.

Bunnel F.L., Tait D.E.N., Flanagan P.W. and Cleve K. van, 1977. Microbial respiration and substrate weight loss, I. A general model of the influences of abiotic variables. Soil Biology and Biochemistry, 9, 33-40.

Cassman K.G. and Munns D.N., 1980. Nitrogen mineralisation as affected by soil moisture, temperature and depth. Soil Sci.Soc. Am.J., 44, 1233-1237.

Driessen P.M., 1988. The QLE primer. A first introduction to Quantified Land Evaluation procedures. Department of Soil Science and Geology, Wageningen Agricultural University.

Ennik, 1982. De bijdrage van witte klaver aan de opbrengst van grasland. Landbouwkundig Tijdschrift, 94, 363-369.

Habets A.S.J. and Oomen G.J.M., 1993. Modellering van de stikstofdynamiek binnen gewasrotaties in de biologische landbouw. Department of Ecological Agriculture, Wageningen Agricultural University.

Haynes R.J., 1986. Mineral nitrogen in the plant-soil system. In: Physiological Ecology, a series of monographs, Texts and Treatises. Academic Press.

Hendriks R.F.A., 1991. Afbraak en mineralisatie van veen; literatuuronderzoek. Rapport 199. DLO-Staring Centrum, Wageningen. 152p.

Hooghart J.C., 1987. Evaporation and weather. Proceedings and information 39. TNO, The Hague.

Janssen B.H., 1984. A simple method for calculating decomposition and accumulation of 'young' soil organic matter. Plant and Soil, 76, 297-304.

Jenkinson D.S., 1977. Studies on the decomposition of plant material in soil. V. The effects of plant cover and soil type on the loss of carbon from 14C labelled ryegrass decomposing under field conditions. Journal of Soil Science, 28, 424-434.

Jenkinson D.S. and Ayanaba A., 1977. Decomposition of carbon-14 labelled plant material under tropical conditions. Soil Science Society of America Journal, 41, 912-915.

Kortleven J., 1963. Kwantitatieve aspecten van humusopbouw en humusafbraak. Versl. Landbouwk. Onderz., 69.1, 1-109.

Ladd J.N., Oades J.M. and Amato M., 1981. Microbial biomass formed from 14C, 15N-labelled plant material decomposing in soils in the field. Soil Biology and Biochemistry, 13, 119-126.

Rijtema P.E., 1980. Nitrogen emission from grassland farms- a model approach. Technical bulletin 119. ICW, Wageningen.

Rijtema P.E. and Kroes J.G., 1991. Some results of nitrogen simulations with the model ANIMO. Fertiliser Research, 27, 189-198.

Tate R.L., 1987. Soil organic matter. New York.

Titulaer H.H.H. and Boone F.R., 1984. Aspects of chemical soil fertility. In: Experiences with three tillage systems on a marine loam soil. Pudoc, Wageningen.

Van Huet H., 1983. Kwantificering en modellering van de stikstofhuishouding in de bodem na bemesting. Nota 1426. ICW, Wageningen.

Van Mil M., 1981. Actual and potential nitrogen fixation in pea and field bean as affected by combined nitrogen. Dissertatie LH-no 870. Landbouw Universiteit Wageningen. 127 p.

Verveda H.W., 1984. Opbouw en afbraak van jonge organische stof in de grond en de stikstofhuishouding onder een vierjarige vruchtwisseling met grasgroenbemester. Interne Mededeling 58. Department of Soil Science and Plant Nutrition, Wageningen Agricultural University.

Yang H.S., 1996. Modelling organic matter mineralization and exploring options for organic matter management in arable farming in northern China. Doctor thesis, Wageningen Agricultural University, The netherlands. 159 pp.


References: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Nitrogen balance

References

Publications


Publications

See also	Symbols	Formulas	Figures	Tables

Some publications related to NDICEA:

Habets A.S.J. en Oomen G.J.M., 1993. Modellering van de stikstofdynamiek binnen gewasrotaties in de biologische landbouw, Vakgroep Ecologische Landbouw, LandbouwUniversiteit Wageningen.

Habets A.S.J. and Oomen G.J.M., 1994. Modelling nitrogen dynamics in crop rotations in ecological agriculture. In: J.J.Neeteson and J.Hassink (eds.), Nitrogen mineralization in agricultural soils; proc.symp. held at the Institute for Soil Fertility Research, Haren, NL, 19-20 April 1993. AB-DLO Thema's, AB-DLO, Haren, pp. 255-268.

Oomen G.J.M., 1995. Nitrogen cycling and nitrogen dynamics in ecological agriculture, Biological Agriculture and Horticulture, 11, 1995, pp. 183-192.

Burgt G.J.H.M. van der, 1997. Tussen voorspelling en waarneming: N-dynamiek onderzocht. In: Ekoland 17 (1997) nr.6.

Burgt G.J.H.M. van der, 1998. Stikstofmodel NDICEA aan praktijk voorgelegd. In: Ekoland 18 (1998) nr.1.

Burgt G.J. van der, 1998. Stikstofdynamiek OBS 1991-1997 met behulp van NDICEA. Louis Bolk Instituut, Driebergen. 30p.

Bokhorst J.G. en Oomen G.J.M., 1998. Verfijning van de bemesting in de biologische landbouw middels modellering van de stikstof dynamiek. Meststoffen, voorjaar 1998.

Oomen G.J.M. and Habets A.S.J., 1998. Using the static whole farm model FARM and the dynamic model NDICEA to integrate arable and animal production. In: Van Keulen H., Lantinga E.A. and Van Laar H.H. (eds.), Mixed farming systems in Europe; Workshop proc., Dronten, NL, 25-28 May 1998. APMinderhoudhoeve-reeks nr.2, Wageningen Agricultural University, pp. 199-206.

Bokhorst J.G. en Oomen G.J.M., 1998. Bemesting in de biologische glastuinbouw; Analyse van de stikstofdynamiek in enkele biologische kassen. Louis Bolk Instituut, Driebergen.

Habets A.S.J., 1998. NDICEA 4.1 model description. 29p.

Burgt G.J. van der, 1999. Stikstofmodellering OBS 1991-1998 met behulp van NDICEA: van kalibratie naar validatie. Louis Bolk Instituut, Driebergen. 34p.

Burgt G.J. van der, 1999. Kalibreren van NDICEA op 7 praktijkbedrijven in 1998. Louis Bolk Instituut, Driebergen. 19p.

Ishikawa S., 2000. Designing crop rotations to improve organic matter and nitrogen balances in arable farming systems using NDICEA: A case study for South Uruguay. MSc. Thesis. Department of Theoretical Production Ecology. Wageningen University and Research Center. 104p.

Bahadur P., 2000. Nirogen and organic matter balances as calculated by the target oriënted models 'QuadMod Plus' and NDICEA to evaluate crop rotations. MSc. Thesis. Department of Theoretical Production Ecology. Wageningen University and Research Center. 140p.

Selaya G., 2000. The role of green manure and crop residues in cropping systems of South Uruguay; A model based exploration. MSc. Thesis. Department of Theoretical Production Ecology. Wageningen University and Research Center. 63p.

Burgt G.J. van der, 2000. Gebruikershandleiding NDICEA 4.2. Concept mei 2000. Louis Bolk Instituut, Driebergen. 47p.

Habets A.S.J., 2000. NDICEA 4.23 model description.


Publications: See also
See also

Introduction

Model overview

Waterbalance

Mineralisation

Nitrogen balance

References

Publications


Appendix 1: Soils file format (*.soi)

See also	Symbols	Formulas	Figures	Tables

Standard soils files are plain ASCI text files. After the 2 header lines every soil takes a single line. Data are separated by spaces. The second header line starts with the total number of soils in the file.

Ndicea 420 Soil File      SMO   GAM   CRc   CRx  TEXT   NLF   RI    BPF

15                    cm3/cm3  /cm2    cm    cm   [-]   [-] mm/wk   [-]

coarse sand             0.395 0.100  54.7 11.66     1     1    35     0

fine sand               0.364 0.029 99.17 22.37     1     1    35     0

loamy fine sand         0.439 0.033 127.4 26.59     1     1    35     0

fine sandy loam         0.504 0.021 150.7 40.07  0.95  0.95    35  0.25

silt loam               0.509 0.019 174.2  33.8  0.90  0.90    35  0.25

loam                    0.503 0.018 61.55 36.19  0.67  0.67    35  0.50

loess loam              0.455 0.017   158 44.29  0.90  0.90    35  0.25

sandy clay loam         0.432 0.010 120.2 33.59  0.87  0.87    35  0.50

silty clay loam         0.475 0.011 114.9 43.96  0.83  0.83    35  0.50

clay loam               0.445 0.006 102.3  45.5  0.78  0.78    35  0.50

light clay              0.453 0.009 76.75 39.34  0.73  0.73    35  0.50

silty clay              0.507 0.007 41.83 27.39  0.67  0.67    35  0.50

basin clay              0.540 0.004 28.39 14.48  0.60  0.60    35  0.50

oligotrofic peat        0.863 0.011 62.69 30.75     1     1    35     0

meso & eutrofic peat    0.863 0.011 88.34  37.2     1     1    35     0

(15 soils in STARIN.SOI)


Appendix 2: Crops file format (*.cro)

See also	Symbols	Formulas	Figures	Tables

Standard crops files are plain ASCI text files. After the 2 header lines every crop takes a single line. Data are separated by spaces. The second header line starts with the total number of crops in the file.

Ndicea 420 Crop File	Arable crops	kg/ha	kgN/ha

74	Year	sow	full	ripe	harv	Prod	DM%	NFixI

Bean	1 	19 	23 	30 	34 	2700 	85.0 	75

...next column	DMdistr [-]	N%dm	Application

Prod	Resi	Root	Prod	Resi	Root	Prod	Resi

0.60 	0.30 	0.10 	4.50 	1.39 	0.80 	0.0 	1.0

...next column	Initial Age	[-]	DM%	Planting

Prod	Resi	Root	ETmax	Resi	Quant	DM%	N%dm

0.99 	1.21 	1.21 	1.1 	85.0 	0 	0 	0

...next column	P2O5%dm	K2O%dm	Planting	[cm]

Prod	Resi	Prod	Resi	P2O5	K2O	RD

1.84 	0.28 	5.73 	1.79 	0.00 	0.00 	60

...continued

(74 crops in ARABLE.CRO)


Appendix 3: Applications file format (*.app)

See also	Symbols	Formulas	Figures	Tables

Standard applications files are plain ASCI text files. After the 2 header lines every application takes a single line. Data are separated by spaces. The second header line starts with the total number of applications in the file.

Ndicea 420 Appl File   Manure                         in DM             in DM

21 APPLICATIONS        ACT   YEAR  WEEK  QUANT  DM%   OM%dm N%dm  IAGE  P2O5% K2O%  Nm%

Cattle Stale               1     1     1   4000   2.5    40    16  1.27   0.8    32    15

Pig Stale                  1     1     1    900     2    25  32.5  1.27   4.5  22.5    31

Sow Stale                  1     1     1      0     1   100    20  1.27     9    25    19

Cattle Slurry              1     1     1  10000   9.5  63.2  4.63  1.95  1.89  5.79   2.5

Pig Slurry                 1     1     1   1700   7.5  66.7  8.67  1.38   5.2  9.07     5

Sow Slurry                 1     1     1   5400   5.5  63.6  6.55  1.57  6.55  6.55     4

Fatt.Calf Slurry           1     1     1   3500     2    75    15  1.57   7.5    12    12

Chicken Slurry             1     1     1     63  13.5  66.7  7.85  1.36  5.45  4.21   4.5

Cattle Manure              1     1     1   5500  21.5  65.1  2.56  1.95  1.77  1.63   0.6

Pig Manure                 1     1     1    700    23  69.6  3.26  1.57  3.91  1.52   0.7

Chicken Manure             1     1     1     18    60  61.7  4.05  1.38  4.72   3.7   0.4

Strew Chicken Manure       1     1     1     25    53    66  2.98  1.57  3.77  2.08   1.3

Fatt.Chicken Manure        1     1     1     10    58  74.1  4.48  1.45  4.14  3.71   0.8

Turkey Manure              1     1     1      0    45  75.6  3.87  1.57  4.29  3.58     1

Horse Manure               1     1     1      0    31  80.7  1.61  1.57  0.97  1.81   0.3

Sheep Manure               1     1     1      0    30    70  2.87  1.57   1.4  5.33   0.7

Mushroom Compost           1     1     1      0    39  51.3  1.79  3.84     2  2.46   0.1

Deep Litter Manure         1     1     1  10000  30.8    65     2  2.45     1     3   0.5

Bloodmeal                  1     1     1   1000    90  77.5    12   0.4     0     0     6

Municipal compost          1     1     1  10000    65    30  1.35   3.4   0.6     1   0.1

Wheat Straw                1     1     1   3000    85    92  0.59  1.41  0.17  1.54     0

(21 applications in MANURE.APP)


Appendix 4: Scenario file format (*.dat)

See also	Symbols	Formulas	Figures	Tables

Scenario files are plain ASCI text files. The third line contains the name of the environment file that is automatically loaded when loading the scenario. Data are separated by spaces.

Ndicea 420 Data File    Default scenario

DEFAULT.DAT

DEFAULT.ENV

----------------------------------------------------------------------

PARAMETERS

 Year Week Weeks ETbare  MWU    pH   CNM   ADM  NDep NFix0   DN0   DNF

    1    1   208  0.45  0.75  7.00  8.30  0.50  40.0  20.0  10.0  0.30

P2O5Dep K2ODep oOM2  oNc2 oAge2  DN02  DNF2

   2.0   1.0      0  4.50 24.00  50.0  0.30

WATERTABLE

  Week   GWT   NGW

     7 100.0  6.00

    29 180.0  0.00

SOIL

                   2   THL   IFi  NMIN   SMO   GAM   CRc   CRx

loamy fine sand         30   100  10.0  0.44 0.033 127.0  27.0

m fine sand             60    62  20.0  0.35 0.040  85.0  18.0

                   2  Text   NLF    FI   BPF

loamy fine sand       1.00  1.00  35.0  0.00

m fine sand           1.00  1.00  35.0  0.00

CROPS:                      sow  fcov  ripe  harv   kg/ha      kgN/ha

                   6  YEAR WEEK1 WEEK2 WEEK3 WEEK4  PRODi   DM% NFIXi

Spring Barley            1     9    21    27    31   3500  85.0     0

Yellow Mustard           1    32    35    48    48   1000 100.0     0

Sugar Beet               2    13    27    37    42  55000  21.8     0

Winter Wheat             2    42    62    82    85   5000  85.0     0

Yellow Mustard           3    34    35    48    48   1000 100.0     0

Potato                   4    15    24    35    37  45000  21.0     0

CROPS:                DMdistr [-]       N%dm              Applied

                   6  PROD  RESI  ROOT  PROD  RESI  ROOT  PROD  RESI

Spring Barley         0.44  0.26  0.30  1.76  0.41  0.80  0.00  0.00

Yellow Mustard        0.72  0.18  0.10  4.00  2.00  0.80  1.00  1.00

Sugar Beet            0.69  0.26  0.05  0.80  2.60  0.80  0.00  1.00

Winter Wheat          0.42  0.28  0.30  2.35  0.59  0.80  0.00  0.00

Yellow Mustard        0.72  0.18  0.10  4.00  2.00  0.80  1.00  1.00

Potato                0.82  0.13  0.05  1.57  2.20  0.80  0.00  1.00

CROPS:                Initial Age      [-]    DM%  Planting

                   6  PROD  RESI  ROOT ETMAX  RESI QUANT   DM%  N%dm

Spring Barley         0.99  1.41  1.21  1.05  85.0     0   0.0  0.00

Yellow Mustard        0.99  1.21  1.21  1.10 100.0     0   0.0  0.00

Sugar Beet            0.99  0.99  1.21  1.10  13.2     0   0.0  0.00

Winter Wheat          0.99  1.41  1.21  1.05  85.0     0   0.0  0.00

Yellow Mustard        0.99  1.21  1.21  1.10 100.0     0   0.0  0.00

Potato                0.99  0.99  1.21  1.10  25.0     0   0.0  0.00

CROPS:                P2O5%       K2O%       Planting    [cm]

                   6  PROD  RESI  PROD  RESI P2O5%  K2O% RDepth

Spring Barley         0.96  0.25  0.72  1.75  0.00  0.00   100

Yellow Mustard        1.15  1.25  3.60  2.00  0.00  0.00    40

Sugar Beet            0.40  0.44  1.11  3.00  0.00  0.00   100

Winter Wheat          1.00  0.19  0.60  1.75  0.00  0.00   100

Yellow Mustard        1.15  1.25  3.60  2.00  0.00  0.00    40

Potato                0.53  0.83  2.47  3.30  0.00  0.00    40

APPLICATIONS

                  12 ACT YR  WK  QUANT   DM% OM%dm  N%dm  IAGE  P2O5% K2O% Nmin%

Old Organic Matter    3   1   1  84000 100.0 100.0  6.00 24.00  0.00  0.00  0.00

Young Organic Matter  3   1   1   5000 100.0 100.0  5.00  6.00  0.00  0.00  0.00

Fresh Organic Matter  3   1   1   1000 100.0 100.0  3.00  1.00  0.00  0.00  0.00

Ploughing             2   1  10    225 100.0 100.0  6.00  2.45  0.00  0.00  0.00

Cattle Manure         1   1  32  22000  21.5  65.1  2.56  1.95  1.77  1.63  0.60

Skim ploughing        2   1  32    175 100.0 100.0  6.00  2.45  0.00  0.00  0.00

Rotary cultivating    2   2  13    200 100.0 100.0  6.00  2.45  0.00  0.00  0.00

Cattle Slurry         1   2  13  30000   9.5  63.2  4.63  1.95  1.89  5.79  2.50

Cultivatoring         2   2  42    125 100.0 100.0  6.00  2.45  0.00  0.00  0.00

Skim ploughing        2   3  33    175 100.0 100.0  6.00  2.45  0.00  0.00  0.00

Cattle Slurry         1   4   9  30000   9.5  63.2  4.63  1.95  1.89  5.79  2.50

Rotary cultivating    2   4  15    200 100.0 100.0  6.00  2.45  0.00  0.00  0.00


Appendix 5: Environment file format (*.env)

See also	Symbols	Formulas	Figures	Tables

Environment files are plain ASCI text files. After the 6 header lines every week takes a single line. Data are separated by spaces. The fourth header line starts with the year and the week number in that year the first week relates to, followed by the total number of weeks in the file.

Ndicea 400 Envi File    De Bilt, Normal

DEFAULT.ENV

Year  week weeks

1985     1   520

  wk    Tc  Rain   ET0

----------------------

   1  -1.3  10.4  -0.8

   2  -1.9   2.1   0.3

   3  -0.9   0.5   0.7

   4   1.3  20.7   0.1

   5   6.0   8.8   1.6

   6   0.0   0.1   2.5

   7  -1.7   0.0   2.3

   8   1.7   0.8   3.5

   9   3.7   4.3   2.4

  10   4.4   6.5   5.0

  11   2.2   6.2   6.7

  12   4.5   4.6   6.4

  13   8.1  29.1   7.1

...continued

(520 weeks in DEFAULT.ENV)


Appendix 6: Irrigation file format (*.irr)

See also	Symbols	Formulas	Figures	Tables

Irrigation files are plain ASCI text files. After the 6 header lines every week with irrigation takes a single line. Data are separated by spaces. The fourth header line starts with the year and the week number in that year the first week with irrigation relates to, followed by the total number of weeks with irrigation in the file.

Ndicea 400 Irri File    Untitled

DEFAULT.IRR

Year  week weeks

1985     1     1

  wk  Irri NIrri

----------------

 179  20.0   0.0

(1 weeks with irrigation in DEFAULT.IRR)


Appendix 7: NMineral file format (*.min)

See also	Symbols	Formulas	Figures	Tables

NMineral files are plain ASCI text files. After the 6 header lines every week with measurements takes a single line. Data are separated by spaces. The fourth header line starts with the year and the week number in that year the first week with measurements relates to, followed by the total number of weeks with measurements in the file.

Ndicea 400 Nmin File    Untitled

DEFAULT.MIN

Year  week weeks

1985     1     8

  wk   Ni1   Ni2

----------------

  10  10.0  20.0

  46   5.0  15.0

  62  10.0  15.0

  98   5.0  25.0

 114  12.0  15.0

 150   5.0  10.0

 166  70.0  20.0

 202  15.0  35.0

(8 weeks with measurements in DEFAULT.MIN)


Appendix: See also
See also

Soils file format (*.soi)

Crops file format (*.cro)

Applications file format (*.app)

Scenario file format (*.dat)

Environment file format (*.env)

Irrigation file format (*.irr)

NMineral file format (*.min)