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LandscapeDNDC
1.36.0
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LandscapeDNDC
1.36.0
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PlaMox simulates the carbon and nitrogen cycle of crops and grass species. Processes are described in a universal way and plants are primarily distinguished by species-specific parameters that can be accessed and calibrated externally. However, for a growing number of specific species (e.g., rice, maize, ...), there exist specific functionalities, which are continuously developed.
PlaMox includes a submodel for photosynthesis calculation based on von Caemmerer and Farquahr 1981. Since the photosynthesis submodel requires a subdaily time step, PlaMox can also only be used with a subdaily time resolution. The recommendation is 24 time steps per day. PlaMox requires further models for:
The following lists include species parameters that might be calibrated in order to represent a specific plant. See the description of respective sections for more details on parameter behaviour.
Photosynthesis:
Nitrogen related parameters:
Allocation related parameters:
Plant development related parameters:
Vernalization related parameters:
Cutting
Stress
Nitrogen uptake
Nitrogen fixation
Respiration
Root exudation
Senescence
Fineroots turnover
water demand
Structure
Available options: Default options are marked with bold letters.
Considered field mangement includes:
For planting events, the following event inputs are considered:
All other quantities are determined by the model:
The N-contents of fine roots, foliage, and structural tissue are set to optimum (parameters NC_FINEROOTS_MAX, NC_FOLIAGE_MAX, and NC_STRUCTURAL_TISSUE_MAX). Mass is only distributed to fine roots and foliage by FRACTION_ROOT and 1 - FRACTION_ROOT.
For harvest events, the following event inputs are considered:
The term wood with regard to the export of roots is neglected and all root parts are considered. The fraction given as remains determines the fraction of straw that remains on the field. If there is not remains fraction given, the amount of straw can be determined via stubble height. If neither remains nor stubble height are given all aboveground biomass is removed from the field.
After grazing the development index of the plant is set to 0.
After cutting the development index of the plant is set to 0.
Phenology of plant growth depends on the plant development stage \( DVS \), which is defined between 0 (germination) and 1 (maturity).
Plant development depends on accumulated growing degree days \( AGDD \), which is the sum of growing degree days over the complete vegetation period:
\[ AGDD = \sum GDD \]
Growing degree days depend on daily mean temperature and a species-specific base temperature:
\[ GDD = (T_{avg} - GDD\_BASE\_TEMPERATURE) \; f_{chill} \]
The factor \(f_{chill} \) retards plant development due to insufficient vernalization (see: vernalization).
Plant development \( \frac{d DVS}{dt} \) is given by:
\[ \frac{d DVS}{dt} = \frac{GDD}{GDD\_MATURITY} \]
In addition to \( DVS \), there exists a mortality state index \( MOS \) that is calculated in the same way as \( DVS \) but interpreted differently and not reset after grazing and cutting events.
Emergence is regulate by accumulated growing degree days \( AGDD \), drought stress and snow. Three conditions must be satisfied for emergence:
\[ AGDD > GDD\_EMERGENCE \\ f_h2o > H2OREF\_FLUSHING \\ snow < 0.01 [m] \]
In case GDD_EMERGENCE is not defined, the plant development index must be greater 5%
Vernalization is only implemented for crops. The following species-specific parameters determine vernalization:
The state of chilling if calculated following [32] (see: Vernalization).
Allocation of assimilated carbon and nitrogen is determined by the plant development stage \( DVS \). PlaMox distinguishes the following compartments:
The plant growth is reduced by a deficient N-content of the leaves, which limits photosynthesis. Then, also the C to N ratio increases.
The fruit fraction \( \theta_{fruit} \) is given by:
\[ \theta_{fruit} = \left\{\begin{array}{cc} 0 & AGDD \le GDD\_GRAIN\_FILLING \\ FRACTION\_FRUIT \cdot \frac{AGDD - GDD\_GRAIN\_FILLING}{GDD\_MATURITY - GDD\_GRAIN\_FILLING} & AGDD > GDD\_GRAIN\_FILLING \end{array} \right. \label{eq2} \]
If there was heatstress during the flowering phase, the fruit fraction is reduced by the factor influence_heat_reduction_grainfilling as calculated in Heat Stress Limitation
m_fruit_max = M_FRUIT_OPT() * (1- influence_heat_reduction_grainfilling)
if no C is being allocated to the fruit
The root fraction \( \theta_{root} \) is constant over time before grain filling starts and then decreases to \( FRACTION\_ROOT \).
\[ \theta_{root} = (1-\theta_{fruit})/(1-FRACTION\_FRUIT) \cdot FRACTION\_ROOT \]
For some species families specific calculations exist:
\[ \theta_{root} = FRACTION\_ROOT - 0.5 \cdot DVS \cdot FRACTION\_ROOT \]
According to [74], root fraction of rice declines from about 20% at seedling stage to 10% at maturity\[ \theta_{root} = \frac{1-\theta_{fruit}}{1 + \frac{1}{RS}} \]
with the root-shoot ratio \( RS \) given by :\[ RS = 0.45 \cdot \left (0.15 + 0.5 \cdot e^{-3 \cdot DVS} \right) \]
\[ \theta_{root} = \frac{1-\theta_{fruit}}{1 + \frac{1}{RS}} \]
with the root-shoot ratio \( RS \) given by :\[ RS = 0.3 - 0.22 \cdot DVS \]
\[ target_{root} = 1 - DVS \cdot 0.5 + DVS \cdot FRACTION\_ROOT \]
\[ value_{root} = \frac{fineroots}{total\_biomass} \]
If the target biomass is larger than the current value,\[ \theta_{root} = target_{root} \]
Stem and leaf fraction are given by:
\[ \theta_{stem} = (1 - \theta_{fruit} - \theta_{root}) \cdot (1-FALEAF)\\ \theta_{leaf} = 1 - \theta_{fruit} - \theta_{root} - \theta_{stem} \]
where \(FALEAF\) is the fraction of straw (leaves + stems) forming leaves.
The reserve/fruit fraction ( \( \theta_{fruit}\)) increases linearly with the plant development in accordance to \( FRACTION\_FRUIT\):
\[ \theta_{fruit} = DVS \cdot FRACTION\_FRUIT \]
A cutting event influences the root/shoot ratio by a factor \( \gamma_{roots}\) (here determined by the fraction of roots \( \theta_{roots}\)):
The root fraction is given by:
\[ \theta_{roots} = (1.0 - \theta_{fruit}) \frac{\gamma_{roots} \; FRACTION\_ROOT}{1 - FRACTION\_FRUIT - (1- \gamma_{roots}) \; FRACTION\_ROOT} \]
As a default or after the first cutting of the year it is
\[ \theta_{roots} = \frac{1.0 - \theta_{fruit}}{1 - FRACTION\_FRUIT} \cdot FRACTION\_ROOT \, . \]
If the current root mass is higher than predicted by the allocation factor, the root allocation factor is decreased exponentially.
The straw fraction is given by
\[ FRACTION\_STRAW = 1 - \theta_{roots} - \theta_{fruit} \, . \]
The current foliage to straw ratio is given by
\[ faleaf = \frac{m_{fol}}{m_{fol}+m_{stem}} \, . \]
If the foliage biomass, \( m_{fol}\), is 0, \( faleaf = 0 \).
If some reserves exist in the stem and after grain filling, some biomass from the stem goes into the grain (reproductive tissue).
Actual photosynthesis is calculated by the external model PhotoFarquhar (Berry Ball). This requires the canopy height specific information of:
The latter two quantities are calculated depending on the rusbisco activity and with the species specific parameters QJVC (Maximum electron transport rate and RubP saturated rate of carboxylation) and QRD25, respectively.
The rubisco activity depends on the species specific parameter VCMAX25 (Maximum RubP saturated rate of carboxylation at 25oC for sun leaves). Further, the following properties are factored in:
Nitrogen availability can be dependent on location specific N-distribution. Only the share \( \phi_L \) of total N that is either located close to the plant or that is homogenously distributed is available.
Daily nitrogen demand is calculated by:
n_opt() \( - \) total_nitrogen()
Nitrogen uptake is calculated for every layer individually. Only layers containing roots are considered.
Temperature dependency of N uptake is given by:
\[ \phi_T = \begin{cases} & 0, \;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\ T < 0.8 \cdot TLIMIT \\ & \frac{t - 0.8 \cdot TLIMIT}{TLIMIT - 0.8 \cdot TLIMIT}, \ 0.8 \cdot TLIMIT < T < TLIMIT \\ & 1, \;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\;\ T > TLIMIT \\ \end{cases} \]
Nitrogen uptake of \( N_x \) is given by;
\[ \frac{dN_x}{dt} = US\_NH4 \cdot N_x \cdot m_{roots} \cdot \phi_L \cdot \phi_T \ \frac{N_x}{N_x + K\_MM\_NITROGEN\_UPTAKE} \]
Two different approaches are considered:
Approach \( NFIX\_RATE > 0.0\)
Approach \( INI\_N\_FIX > 0.0\)
Maintenance respiration is calculated after [61] :
Growth respiration:
\[ C_{resp} = \frac{\text{FYIELD}}{1.0 - \text{FYIELD}} * carbonuptake \]
Senescence calculates fluxes from living to dead plant tissue separately for above- and belowground plant parts.
List of senescence processes affecting aboveground tissue:
\[ \Phi_d = SENESCENCE\_DROUGHT \cdot \phi_d \]
The drought stress factor \( \phi_d \) is given by: Linear relationship
\[ \Phi_h = SENESCENCE\_HEAT \cdot (1 - \phi_{h}) \]
The heat stress factor \( \phi_h \) is given by: Heat factor
Frost stress for \( T < 0 \) is given by:
\[ \Phi_f = \begin{cases} & 0, T >= 0 \\ & SENESCENCE\_FROST \cdot \frac{T}{-20}, -20 < T < 0 \\ & SENESCENCE\_FROST, T <= -20 \\ \end{cases} \]
\[ \Phi_h = SENESCENCE\_HEAT \cdot (1 - \phi_{h}) \]
The heat stress factor \( \phi_h \) is given by: Heat factor
Grass:
\[ \Phi_{a,leaf} = SENESCENCE\_AGE \cdot DVS \\ \Phi_{a,stem} = SENESCENCE\_AGE \cdot DVS \]
Crops:
\[ \Phi_{a,leaf} = SENESCENCE\_AGE \cdot \frac{GDD - GDD\_GRAIN\_FILLING}{GDD\_MATURITY - GDD\_GRAIN\_FILLING} \\ \Phi_{a,stem} = 0.0 \]
List of senescence processes affecting belowground tissue:
\[ \Phi_d = SENESCENCE\_DROUGHT \cdot \phi_d \]
Frost stress for \( T < 0 \) is given by:
\[ \Phi_f = \begin{cases} & 0, T >= 0 \\ & SENESCENCE\_FROST \cdot \frac{T}{-20}, -20 < T < 0 \\ & SENESCENCE\_FROST, T <= -20 \\ \end{cases} \]
Age or temperature stress
Calculates potential transpiration on
a) water use efficiency and carbon uptake:
b) stomatal conductance and vapour pressure deficit:
If an hourly timestep is chosen, this is done hourly. However, only the accumulated potential transpiration is stored.
Roots are represented in a one-dimensional way by the fine root mass distribution and the total fine root mass.
Currently available distribution functions for vertical root distribution:
The environmental function is used for \( ROOTS\_ENVIRONMENTAL = true\). If \( ROOTS\_ENVIRONMENTAL = false\), the exponential function is used for \( EXP\_ROOT\_DISTRIBUTION > 0\). If \( ROOTS\_ENVIRONMENTAL = false\) and \( EXP\_ROOT\_DISTRIBUTION <= 0\), the sigmoid function is used.
See Sink-strength driven root distribution.
See Empirical root growth distribution
Gaseous conductivity of roots is expressed by an root aerenchyme transport \( r_{tc}\) coefficient:
\[ r_{tc} = m_r \cdot RS\_CONDUCT \]
Ground coverage of grass is always assumed to be 100%
Ground coverage of crops is estimated by lai:
\[ gc = \frac{lai}{3}^{0.5} \]
Full cover is reached with a leaf area index of three (FAO).
Calculates specific leaf area weight sla kg m-2 in each canopy layer:
\[ sla = SLAMAX \cdot ( 1 - dvs \cdot SLADECLINE \cdot dvsMort) \]
For selected species (mungbean, rice, grass), specific formulations exist.If the plant experiences heat stress during the critical time around flowering, the pod set is reduced. The approach followes the ones introduced by Challinor et al. 2005 and Nendel 2011.
The relevant temperature for this heat stress factor is the temperature during the photoactive period ( \( T_{d}\) ), since it affects the time during which flowers are open.
\[ T_d = T_{max} - \frac{T_{max} - T_{min}}{4} \]
(following Mirschel & Wenke (2007)).
Challinor et al. 2005 introduced a variable Temperature threshold \( T_{crit} \) dependent on timing and duration of the heat stress during the flowering period.
The daily influence ( \( heat_{d}\) ) of the heat limitation is calculated dependent on the daily fraction of flowers open:
\[ heat_{daily} = 1 - (\frac{(T_d - T_{crit})}{(T_{zero} - T_{crit})}) * frac\_flower; \]
The daily fraction of flowers newly opened:
\[ frac\_flower = openFlowers_{today} - openFlowers_{yesterday} \]
The open Flowers on a specific day after flowering (daf) (Moriondo et al. 2011) :
\[ openFlowers = \frac{1}{(1 + \frac{1}{0.015 - 1} * \exp{-1.4 * daf})}; \]
The overall influence on the grain reduction is:
\[ influence\_heat\_reduction\_grainfilling = min(heat_{daily}) \]
Heat factor \( \phi_h \) is given by:
\[ \phi_h = 1 - \frac{1}{1 + e^{-2 (T_{leaf} - PSNTMAX)}} \]
Nitrogen deficiency factor \( \phi_n \) is given by:
\[ \phi_n = \frac{c_{N,fol}}{c_{N,fol,opt}}^{N\_DEF\_FACTOR} \]
The age factor is calculated dependend on the growing degree days (GDD) (see vernalization()), the minimum temperature sum for
foliage activity onset (parameter GDDFOLSTART) and temperature degree days for full plant development .
For grass:
\[ f_{a} = 1.0 - \frac{(\text{GDDFOLSTART} - \text{GDD})}{\text{GDDFOLSTART}} \]
For all other species:
\[ f_{a} = \text{max}\left(0.0, 1.0 - \frac{\text{GDD} - (0.9 * GDD\_MATURITY)}{GDD\_MATURITY - (0.9 * GDD\_MATURITY)} \right) \]
Grass: foliage nitrogen concentration is constant (from species parameter NC_FOLIAGE_MAX)
Crops: foliage nitrogen concentration is highest at planting (NC_FOLIAGE_MAX) and decreases until harvest to NC_FOLIAGE_MIN.
1.8.13