Crop modeling in the Community Land Model

Contact: Peter Lawrence

The CLM crop model was developed to improve the fully coupled simulations of the Community Earth System Model (CESM1) and to help begin answering questions about changes in food, energy, and water resources in response to changes in climate, environmental conditions, and land use within the CESM modeling framework. There are four versions of the model: CLM 4CLM 4.5CLM post 4.5, and CLM5 (currently in development), and numerous ongoing projects are using CLM Crop, including the Land Use Model Intercomparison Project (LUMIP), the THESIS Crop Yield Tool, the Agricultural Model Intercomparison and Improvement Project (AgMIP), and the Geoengineering Model Intercomparison Project (GeoMIP).

CLM 4 version

CLM crop was initially incorporated into the CLM4CN model (Oleson, Lawrence et al. 2010) by replacing the unmanaged C3 crop plant functional type (PFT) which represented all crops globally, with a small number of interactive managed crops over temperate northern hemisphere latitudes (Levis, Bonan et al. 2012). The CLM4CN crop model introduced the managed crop types of corn, soybean, and spring wheat (which represented more generally temperate cereals). The new crops reside on their own soil column, independent to the remaining natural vegetation that shares a single soil column. These crops were chosen based on the availability of their corresponding algorithms in the crop model AgroIBIS (Kucharik and Brye 2003). The main additions to CLM4CN involved the addition of the AgroIBIS crop phenology and allocation algorithms to those of the existing algorithms used for natural vegetation. The AgroIBIS algorithms consist 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.

Phase 1 Planting to Start of Leaf Emergence: Crops are planted in the model within a crop-specific planting window once the 10-day running mean and minimum temperature counters reach crop specific temperature thresholds. If the temperature thresholds are not reached during the planting window then the crop is planted at the end of the planting window. For corn the planting window is from April 1st to June 14th, with a running mean planting temperature of 10oC and a minimum planting temperature of 6oC. At planting, each crop is assigned 1g seed C/m2 which is transferred to the leaves upon leaf emergence. An equivalent amount of seed N is assigned given the crop’s C to N ratio for leaves.

Phase 2 Leaf Emergence to Beginning of Grain Fill: Leaf emergence occurs once the soil Growing Degree Day (GDD) count starting from the planting date reaches a fraction of the maturity GDD value. The fraction of the maturity GDD, the GDD base temperature, and the calculation of the maturity GDD are all crop specific. For corn the leaf emergence fraction of the maturity GDD is 3%, the GDD base temperature is 8oC, and the maturity GDD is 0.85 * the 20 year running mean of the GDD count for the growing season of April 1st to September 30th within the range 950 – 1850odays. At leaf emergence, leaf onset as defined in the CLM4CN model occurs, at which point all seed C and N pools are transferred to the leaf C and N pools. Photosynthesis and transpiration then follow other vegetation types in CLM4CN based on (Farquhar, von Caemmerer et al. 1980) and modified by (Collatz, Ball et al. 1991). For crop PFTs the CN nitrogen down regulation is disabled with Vcmax25 prescribed rather than calculated within the model. The carbon assimilated from photosynthesis is allocated to fine roots, leaves, and live stems with dynamic fractions based on the accumulating GDD value up to a peak leaf area index (LAI) value. Once peak LAI is reached allocation then all allocation goes to fine roots.

Phase 3 Grain Fill to Maturity and Harvest: The grain fill phase is triggered once a 2m air temperature GDD count from the planting date reaches a crop specific fraction of the maturity GDD value. For corn this fraction is an empirical function based on the grid cell maturity GDD within the range 55% to 65% of the maturity GDD. During the grain fill phase the allocation rules are changed to gradually reduce allocation to leaves and live stems with the residual fraction used for filling the grain C and N pools with the CN ratios of the grain the same as live wood in CLM4CN. During the grain fill period LAI also declines in response to the background litterfall rate in the same manner as simulated for natural vegetation PFTs in CLM4CN with a crop specific turnover time. Crop maturity is reached once the 2m air temperature GDD count reaches the crop specific maturity GDD or the number of days from planting exceeds the crop specific maximum. For corn the maximum days from planting is 165. At harvest the grain, leaf and live stem C and N pools are all routed directly to the column litter pool with the dormant crop pools set to zero.

CLM4 resources


CLM 4.5 version

In the CLM4.5 version of the CLM crop model the standard CLM calculation of Vcmax25 was reintroduced to crops with new fertilizer management and nitrogen fixation by soybeans (Oleson, Lawrence et al. 2013). The fertilizer functionality adds a central U.S. annual crop specific amount of nitrogen directly to the soil mineral nitrogen pool for each crop. In order to prevent large nitrogen losses through denitrification the annual fertilizer amount is applied continuously over the 20 days from leaf emergence. The total annual fertilizer amount for corn is 15 gN/m2. The nitrogen fixation by soybeans follows the SWAT model of (Neitsch, Arnold et al. 2005), depending on soil moisture, nitrogen availability, and growth stage.

The CLM 4.5 version of CLM crop also includes irrigation functionality loosely following (Ozdogan, Rodell et al. 2010) where irrigation infrastructure is prescribed and soil moisture is limiting for photosynthesis. Irrigated and rainfed versions of the same crop in a grid cell have their own soil columns to allow independent treatment of the different crop managements. On the irrigated soil column the model calculates the difference between the current and the stress free target soil moisture values over the root zone once a day at 6am local time. Any deficit in soil moisture is added to the soil surface over a four-hour irrigation period taken from the surface water runoff. If there is insufficient surface runoff to supply the soil moisture deficit then conservation of water is maintained through negative surface runoff.

CLM 4.5 resources


CLM post 4.5 version

In the CLM post 4.5 version of the crop model used in the BRACE and AgMIP Global Gridded Crop Model Intercomparison (GGCMI) studies, extra tropical crops were added to the temperate corn, soybean, and spring wheat crops of CLM 4.5. The new crops include sugarcane, rice, cotton, tropical corn, and tropical soybean using the CLM4.5 parameterizations with modified parameter values from (Badger and Dirmeyer 2015). Specifically for sugarcane and tropical corn the CLM4.5 temperate corn functional form is used because all three are C4 plants. For tropical soybean the temperate soybean functional form is used and for rice and cotton the spring wheat functional form is used. The BRACE studies detail the use of the CLM post 4.5 crop model for assessing the impacts of changes in climate, atmospheric CO2, N fertilizer and irrigation on crop yield and water demand (Levis, Badger et al. 2016).

CLM post 4.5 resources


CLM 5 version

The currently in development CLM 5 crop model will include new additional functionality to represent the new Land Use and Land Cover Change time series prescribed by the Land Use Model Intercomparison Project (LUMIP) which will be part of all CESM2 simulations in CMIP6 (Lawrence, Hurtt et al. 2016). The new crop model components will prescribe transient total crop area, crop fractions, irrigation fraction, and N fertilizer geographically by grid cell, crop, and year along a given scenario. Following suggestions by (Levis 2014) and (Levis, Badger et al. 2016) new heat stress functionality may be needed to account for the impacts of climate change currently not represented in the CLM crop model. A new crop representation has been developed for winter wheat that includes vernalization and cold damage functions. Analysis in the BRACE and AgMIP projects have also identified crop yield simulation issues for rice in colder mid to high latitudes.

CLM 5 resources


Ongoing Projects with CLM Crop

  • CMIP6 LUMIP CLM5 - Investigators: David Lawrence, Peter Lawrence and Danica Lombardozzi
  • THESIS Crop Yield Tool - Investigators: Peter Lawrence, Brian O’Neill, Xiaolin Ren, Matthias Weitzel
  • AgMIP GGCMI - Investigators: Peter Lawrence, Yaqiong Lu
  • GeoMIP - Investigators: Alan Robock, Lili Xia
  • Winter Wheat - Investigators: Yaqiong Lu
  • Rice - Investigators: Peter Lawrence, Yaqiong Lu, Fang Li
  • Heat and Drought Stress Crop Damage - Investigators: Peter Lawrence, Yaqiong Lu


Badger, A. M. and P. A. Dirmeyer (2015). "Climate response to Amazon forest replacement by heterogeneous crop cover." Hydrology and Earth System Sciences 19(11): DOI:10.5194/hess-5119-4547-2015.

Collatz, G. J., J. T. Ball, C. Grivet and J. A. Berry (1991). "Physiological and environmental regulation of stomatal conductance, photosynthesis and transpiration: A model that includes a laminar boundary layer." Agricultural and Forest Meteorology 54: 107-136.

Farquhar, G. D., S. von Caemmerer and J. A. Berry (1980). "A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species." Planta 149(1): 78-90.

Kucharik, C. J. and K. R. Brye (2003). "Integrated BIosphere Simulator (IBIS) Yield and Nitrate Loss Predictions for Wisconsin Maize Receiving Varied Amounts of Nitrogen Fertilizer." Journal of Environmental Quality 32(1): DOI:10.2134/jeq2003.2470.

Lawrence, D. M., G. C. Hurtt, A. Arneth, V. Brovkin, K. V. Calvin, A. D. Jones, C. D. Jones, P. J. Lawrence, N. De Noblet-Ducoudre, J. Pongratz, S. I. Seneviratne and E. Shevliakova (2016). "The Land Use Model Intercomparison Project (LUMIP): Rationale and experimental design." Geoscientific Model Development in review.

Levis, S. (2014). "Crop heat stress in the context of Earth System modeling." Environmental Research Letters 9(6): DOI:10.1088/1748-9326/1089/1086/061002.

Levis, S., A. Badger, B. Drewniak, C. Nevison and X. Ren (2016). "CLMcrop yields and water requirements: avoided impacts by choosing RCP 4.5 over 8.5." Climatic Change: DOI: 10.1007/s10584-10016-11654-10589.

Levis, S., G. B. Bonan, E. Kluzek, P. E. Thornton, A. Jones, W. J. Sacks and C. J. Kucharik (2012). "Interactive Crop Management in the Community Earth System Model (CESM1): Seasonal Influences on Land–Atmosphere Fluxes." Journal of Climate 25(14): DOI: 10.1175/JCLI-D-1111-00446.00441.

Neitsch, S. L., J. G. Arnold, J. R. Kiniry and J. R. Williams (2005). Soil and Water Assessment Tool, Theoretical Documentation: Version 2005. Temple, TX, USDA Agricultural Research Service and Texas A&M Blackland Research Center.

Oleson, K. W., D. M. Lawrence, G. B. Bonan, B. Drewniak, M. Huang, C. D. Koven, S. Levis, L. Fang, W. J. Riley, Z. M. Subin, S. C. Swenson and P. Thornton (2013). Technical Description of version 4.5 of the Community Land Model (CLM). Boulder CO, NCAR.

Oleson, K. W., D. M. Lawrence, G. B. Bonan, M. G. Flanner, E. Kluzek, P. J. Lawrence, S. Levis, S. C. Swenson and P. E. Thornton (2010). Technical Description of version 4.0 of the Community Land Model (CLM). Boulder, CO, National Center for Atmospheric Research: 257.

Ozdogan, M., M. Rodell, H. K. Beaudoing and D. L. Toll (2010). "Simulating the Effects of Irrigation over the United States in a Land Surface Model Based on Satellite-Derived Agricultural Data." Journal of Hydrometeorology 11(1): DOI: 10.1175/2009JHM1116.1171.