### 2.26.2.3. Phenology[¶](#phenology "Permalink to this headline")

CLM5-BGC includes evergreen, seasonally deciduous (responding to changes in day length), and stress deciduous (responding to changes in temperature and/or soil moisture) phenology algorithms (Chapter [2.20](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.html#rst-vegetation-phenology-and-turnover)). CLM5-BGC-crop uses the AgroIBIS crop phenology algorithm, consisting of three distinct phases.

Phase 1 starts at planting and ends with leaf emergence, phase 2 continues from leaf emergence to the beginning of grain fill, and phase 3 starts from the beginning of grain fill and ends with physiological maturity and harvest.

#### 2.26.2.3.1. Planting[¶](#planting "Permalink to this headline")

All crops must meet the following requirements between the minimum planting date and the maximum planting date (for the northern hemisphere) in [Table 2.26.2](#table-crop-phenology-parameters):

(2.26.1)[¶](#equation-25-1 "Permalink to this equation")\\\[\\begin{split}\\begin{array}{c} {T\_{10d} >T\_{p} } \\\\ {T\_{10d}^{\\min } >T\_{p}^{\\min } } \\\\ {GDD\_{8} \\ge GDD\_{\\min } } \\end{array}\\end{split}\\\]

where \\({T}\_{10d}\\) is the 10-day running mean of \\({T}\_{2m}\\), (the simulated 2-m air temperature during each model time step) and \\(T\_{10d}^{\\min}\\) is the 10-day running mean of \\(T\_{2m}^{\\min }\\) (the daily minimum of \\({T}\_{2m}\\)). \\({T}\_{p}\\) and \\(T\_{p}^{\\min }\\) are crop-specific coldest planting temperatures ([Table 2.26.2](#table-crop-phenology-parameters)), \\({GDD}\_{8}\\) is the 20-year running mean growing degree-days (units are °C day) tracked from April through September (NH) above 8°C with maximum daily increments of 30 degree-days (see equation [(2.26.3)](#equation-25-3)), and \\({GDD}\_{min }\\)is the minimum growing degree day requirement ([Table 2.26.2](#table-crop-phenology-parameters)). \\({GDD}\_{8}\\) does not change as quickly as \\({T}\_{10d}\\) and \\(T\_{10d}^{\\min }\\), so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the \\({GDD}\_{8}\\) threshold is met. If the requirements in equation [(2.26.1)](#equation-25-1) are not met by the maximum planting date, crops are still planted on the maximum planting date as long as \\({GDD}\_{8} > 0\\). In the southern hemisphere (SH) the NH requirements apply 6 months later.

At planting, each crop seed pool is assigned 3 gC m\-2 from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the PFT’s C to N ratio for leaves (\\({CN}\_{leaf}\\) in [Table 2.26.3](#table-crop-allocation-parameters); this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, \\({GDD}\_{mat}\\), according to the following AgroIBIS rules:

(2.26.2)[¶](#equation-25-2 "Permalink to this equation")\\\[\\begin{split}\\begin{array}{lll} GDD\_{{\\rm mat}}^{{\\rm corn,sugarcane}} =0.85 GDD\_{{\\rm 8}} & {\\rm \\; \\; \\; and\\; \\; \\; }& 950 <GDD\_{{\\rm mat}}^{{\\rm corn,sugarcane}} <1850{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm mat}}^{{\\rm spring\\ wheat,cotton}} =GDD\_{{\\rm 0}} & {\\rm \\; \\; \\; and\\; \\; \\; } & GDD\_{{\\rm mat}}^{{\\rm spring\\ wheat,cotton}} <1700{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm mat}}^{{\\rm temp.soy}} =GDD\_{{\\rm 10}} & {\\rm \\; \\; \\; and\\; \\; \\; } & GDD\_{{\\rm mat}}^{{\\rm temp.soy}} <1900{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm mat}}^{{\\rm rice}} =GDD\_{{\\rm 0}} & {\\rm \\; \\; \\; and\\; \\; \\; } & GDD\_{{\\rm mat}}^{{\\rm rice}} <2100{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm mat}}^{{\\rm trop.soy}} =GDD\_{{\\rm 10}} & {\\rm \\; \\; \\; and\\; \\; \\; } & GDD\_{{\\rm mat}}^{{\\rm trop.soy}} <2100{}^\\circ {\\rm days} \\end{array}\\end{split}\\\]

where \\({GDD}\_{0}\\), \\({GDD}\_{8}\\), and \\({GDD}\_{10}\\) are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26 degree-days (for \\({GDD}\_{0}\\)) or 30 degree-days (for \\({GDD}\_{8}\\) and \\({GDD}\_{10}\\)). Equation [(2.26.3)](#equation-25-3) shows how we calculate \\({GDD}\_{0}\\), \\({GDD}\_{8}\\), and \\({GDD}\_{10}\\) for each model timestep:

(2.26.3)[¶](#equation-25-3 "Permalink to this equation")\\\[\\begin{split}\\begin{array}{lll} GDD\_{{\\rm 0}} =GDD\_{0} +T\_{2{\\rm m}} -T\_{f} & \\quad {\\rm \\; \\; \\; where\\; \\; \\; } & 0 \\le T\_{2{\\rm m}} -T\_{f} \\le 26{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm 8}} =GDD\_{8} +T\_{2{\\rm m}} -T\_{f} -8 & \\quad {\\rm \\; \\; \\; where\\; \\; \\; } & 0 \\le T\_{2{\\rm m}} -T\_{f} -8\\le 30{}^\\circ {\\rm days} \\\\ GDD\_{{\\rm 10}} =GDD\_{10} +T\_{2{\\rm m}} -T\_{f} -10 & \\quad {\\rm \\; \\; \\; where\\; \\; \\; } & 0 \\le T\_{2{\\rm m}} -T\_{f} -10\\le 30{}^\\circ {\\rm days} \\end{array}\\end{split}\\\]

where, if \\({T}\_{2m}\\) - \\({T}\_{f}\\) takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. \\({T}\_{f}\\) is the freezing temperature of water and equals 273.15 K, \\({T}\_{2m}\\) is the 2-m air temperature in units of K, and _GDD_ is in units of degree-days.

#### 2.26.2.3.2. Leaf emergence[¶](#leaf-emergence "Permalink to this headline")

According to AgroIBIS, leaves may emerge when the growing degree-days of soil temperature to 0.05 m depth (\\(GDD\_{T\_{soi} }\\) ), which is tracked since planting, reaches 1 to 5% of \\({GDD}\_{mat}\\) (see Phase 2 % \\({GDD}\_{mat}\\) in [Table 2.26.2](#table-crop-phenology-parameters)). The base temperature threshold values for \\(GDD\_{T\_{soi} }\\) are listed in [Table 2.26.2](#table-crop-phenology-parameters) (the same base temperature threshold values are also used for \\(GDD\_{T\_{{\\rm 2m}} }\\) in section [2.26.2.3.3](#grain-fill)), and leaf emergence (crop phenology phase 2) starts when this threshold is met. Leaf onset occurs in the first time step of phase 2, at which moment all seed C is transferred to leaf C. Subsequently, the leaf area index generally increases throughout phase 2 until it reaches a predetermined maximum value. Stem and root C also increase throughout phase 2 based on the carbon allocation algorithm in section [2.26.2.4.1](#leaf-emergence-to-grain-fill).

#### 2.26.2.3.3. Grain fill[¶](#grain-fill "Permalink to this headline")

The grain fill phase (phase 3) begins in one of two ways. The first potential trigger is based on temperature, similar to phase 2. A variable tracked since planting, similar to \\(GDD\_{T\_{soi} }\\) but for 2-m air temperature, \\(GDD\_{T\_{{\\rm 2m}} }\\), must reach a heat unit threshold, _h_, of of 40 to 65% of \\({GDD}\_{mat}\\) (see Phase 3 % \\({GDD}\_{mat}\\) in [Table 2.26.2](#table-crop-phenology-parameters)). For crops with the C4 photosynthetic pathway (temperate and tropical corn, sugarcane), the \\({GDD}\_{mat}\\) is based on an empirical function and ranges between 950 and 1850. The second potential trigger for phase 3 is based on leaf area index. When the maximum value of leaf area index is reached in phase 2 ([Table 2.26.3](#table-crop-allocation-parameters)), phase 3 begins. In phase 3, the leaf area index begins to decline in response to a background litterfall rate calculated as the inverse of leaf longevity for the PFT as done in the BGC part of the model.

#### 2.26.2.3.4. Harvest[¶](#harvest "Permalink to this headline")

Harvest is assumed to occur as soon as the crop reaches maturity. When \\(GDD\_{T\_{{\\rm 2m}} }\\) reaches 100% of \\({GDD}\_{mat}\\) or the number of days past planting reaches a crop-specific maximum ([Table 2.26.2](#table-crop-phenology-parameters)), then the crop is harvested. Harvest occurs in one time step using the BGC leaf offset algorithm.

Table 2.26.2 Crop phenology and morphology parameters for the active crop plant functional types (PFTs) in CLM5BGCCROP. Numbers in the first row correspond to the list of PFTs in [Table 2.26.1](#table-crop-plant-functional-types).[¶](#id21 "Permalink to this table")           
|  | temperate corn
 | spring wheat

 | temperate soybean

 | cotton

 | rice

 | sugarcane

 | tropical corn

 | tropical soybean

 | miscanthus

 | switchgrass

 |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| IVT

 | 17, 18

 | 19, 20

 | 23, 24

 | 41, 42

 | 61, 62

 | 67, 68

 | 75, 76

 | 77, 78

 | 71, 72

 | 73, 74

 |
| \\(Date\_{planting}^{min}\\)

 | April 1

 | April 1

 | May 1

 | April 1

 | Janurary 1

 | Janurary 1

 | March 20

 | April 15

 | April 1

 | April 1

 |
| \\(Date\_{planting}^{max}\\)

 | June 15

 | June 15

 | June 15

 | May 31

 | Feburary 28

 | March 31

 | April 15

 | June 31

 | June 15

 | June 15

 |
| \\(T\_{p}\\)(K)

 | 283.15

 | 280.15

 | 286.15

 | 294.15

 | 294.15

 | 294.15

 | 294.15

 | 294.15

 | 283.15

 | 283.15

 |
| \\(T\_{p}^{ min }\\)(K)

 | 279.15

 | 272.15

 | 279.15

 | 283.15

 | 283.15

 | 283.15

 | 283.15

 | 283.15

 | 279.15

 | 279.15

 |
| \\({GDD}\_{min}\\) (degree-days)

 | 50

 | 50

 | 50

 | 50

 | 50

 | 50

 | 50

 | 50

 | 50

 | 50

 |
| base temperature for GDD (°C)

 | 8

 | 0

 | 10

 | 10

 | 10

 | 10

 | 10

 | 10

 | 8

 | 8

 |
| \\({GDD}\_{mat}\\) (degree-days)

 | 950-1850

 | ≤ 1700

 | ≤ 1900

 | ≤ 1700

 | ≤ 2100

 | 950-1850

 | 950-1850

 | ≤ 2100

 | 950-1850

 | 950-1850

 |
| Phase 2 % \\({GDD}\_{mat}\\)

 | 3%

 | 5%

 | 3%

 | 3%

 | 1%

 | 3%

 | 3%

 | 3%

 | 3%

 | 3%

 |
| Phase 3 % \\({GDD}\_{mat}\\)

 | 65%

 | 60%

 | 50%

 | 50%

 | 40%

 | 65%

 | 50%

 | 50%

 | 40%

 | 40%

 |
| Max. growing season length (\\(mxmat\\))

 | 165

 | 150

 | 150

 | 160

 | 150

 | 300

 | 160

 | 150

 | 210

 | 210

 |
| \\(z\_{top}^{\\max }\\) (m)

 | 2.5

 | 1.2

 | 0.75

 | 1.5

 | 1.8

 | 4

 | 2.5

 | 1

 | 2.5

 | 2.5

 |
| SLA (m 2 leaf g \-1 C)

 | 0.05

 | 0.035

 | 0.035

 | 0.035

 | 0.035

 | 0.05

 | 0.05

 | 0.035

 | 0.057

 | 0.049

 |
| \\(\\chi \_{L}\\) index

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 | \-0.5

 |
| grperc

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 | 0.11

 |
| flnr

 | 0.293

 | 0.41

 | 0.41

 | 0.41

 | 0.41

 | 0.293

 | 0.293

 | 0.41

 | 0.293

 | 0.293

 |
| fcur

 | 1

 | 1

 | 1

 | 1

 | 1

 | 1

 | 1

 | 1

 | 1

 | 1

 |

Notes:

*   \\(Date\_{planting}^{min}\\) and \\(Date\_{planting}^{max}\\) are the minimum and maximum planting dates (defining the “sowing window”) in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. [2.26.2.3.1](#planting).) These parameters can also be set with more geographic variation via input map stream files `stream_fldFileName_swindow_start` and `stream_fldFileName_swindow_end`.
    
*   \\(T\_{p}\\) and \\(T\_{p}^{ min }\\) are crop-specific average and coldest planting temperatures, respectively. (See Sect. [2.26.2.3.1](#planting).)
    
*   \\(GDD\_{min}\\) is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. [2.26.2.3.1](#planting) for details.
    
*   \\(GDD\_{mat}\\) is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity.
    
*   \\(mxmat\\) is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached \\(GDD\_{mat}\\).
    
*   \\(z\_{top}^{\\max }\\) is the maximum top-of-canopy height of a crop (see Sect. [2.2.1.3](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.html#vegetation-structure)).
    
*   SLA is specific leaf area (see Chapter [2.10](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.html#rst-photosynthetic-capacity)).
    
*   \\(\\chi \_{L}\\) is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. (See Sect. [2.3.1](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.html#canopy-radiative-transfer).)
    
*   grperc is the growth respiration factor (see Sect. [2.17.1.2](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.html#growth-respiration)).
    
*   flnr is the fraction of leaf N in the Rubisco enzyme (a.k.a. \\(N\_{cb}\\) in Sect. [2.10.2.1](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.html#plant-nitrogen)).
    
*   fcur is the fraction of allocation that goes to currently displayed growth (i.e., that is not sent to storage). See Sect. [2.19.4](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.html#carbon-allocation-to-new-growth).
    

