通用陆面CoLM模式模型手册

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1、 The Common Land Model (CoLM) Technical & User Guide Yongjiu Dai & Duoying Ji School of Geography Beijing Normal University Beijing 100875 China E-mail: yongjiudai@ duoyingji@ July 7, 2008 Contents 1. Introduction 2. Creating and

2、 Running the Executable 2.1 Specification of script environment variables and header file 2.2 Surface data making 2.3 Initial data making 2.4 Time-loop calculation 3. CoLM Surface Dataset 4. CoLM Atmospheric Forcing Dataset 4.1 GSWP2 forcing dataset 4.2 PRINCETON forcing dataset 4.3

3、 Temporal interpolation of the forcing data 5. CoLM Model Structure and Parallel Implementation 5.1 CoLM Model Structure 5.2 CoLM MPI Parallel Design 5.3 CoLM MPI Parallel Implementation 5.4 CoLM Source Code and Subroutines Outline 6. CoLM Parameter and Variables 6.1 Model Parameters 6

4、.2 Time invariant model variables 6.3 TUNABLE constants 6.4 Time-varying state variables 6.5 Forcing 6.6 Fluxes 7. Examples 7.1 Single Point Offline Experiment 7.2 Global Offline Experiment with GSWP2 Dataset Table 1: Model directory structure Table 2: define.h CPP tokens

5、Table 3: Namelist variables for initial data making Table 4: Namelist variables for Time-loop calculation Table 5: The list of raw data available Table 6: Description of 24-category (USGS) vegetation categories Table 7: Description of 17-category soil categories Table 8: The re

6、lative amounts of sand, soil, and clay Table 9: netCDF File Information of the Processed Atmospheric Forcing Data Table 10: Source code and Subroutines Outline Table 11: Dimension of model array Table 12: Control variables to determine updating on time steps Table 13: Model time invarian

7、t variables Table 14: Model TUNABLE constants Table 15: Run calendar Table 16: Time-varying Variables for restart run Table 17: Atmospheric Forcing Table 18: Model output in xy Grid Form Figure 1: Flow chart of the surface data making Figure 2: Flow chart of the initial data making

8、Figure 3: Flow chart of the time-looping calculation Figure 4: Diagram of the domain partition at surface data making Figure 5: Diagram of the domain partition at time-looping calculation Figure 6: Diagram of the patches and grids mapping relationship 1. Introduction This user’s guide pr

9、ovide the user with the coding implementation, and operating instructions for the Common Land Model (CoLM) which is the land surface parameterization used in offline mode or with the global climate models and regional climate models. The development of the Common Land Model (hereafter we call CL

10、M initial version) can be described as the work of a community effort. Initial software specifications and development focused on evaluating the best features of existing land models. The model performance has been validated in very extensive field data included sites adopted by the Project for Inte

11、rcomparison of Land-surface Parameterization Schemes (Cabauw, Valdai, Red-Arkansas river basin) and others [FIFE, BOREAS, HAPEX-MOBILHY, ABRACOS, Sonoran Desert, GSWP, LDAS]. The model has been coupled with the NCAR Community Climate Model (CCM3). Documentation for the CLM initial version is provide

12、d by Dai et al. (2001) while the coupling with CCM3 is described in Zeng et al. (2002). The model was introduced to the modeling community in Dai et al. (2003). The CLM initial version was adopted as the Community Land Model (CLM2.0) for use with the Community Atmosphere Model (CAM2.0) and versio

13、n 2 of the Community Climate System Model (CCSM2.0). The current version of Community Land Model, CLM3.0, was released in June 2004 as part of the CCSM3.0 release (http://www.ccsm.ucar.edu/models/ccsm3.0/clm3/). The Community Land Model (CLM3.0) is radically different from CLM initial version, parti

14、cularly from a software engineering perspective, and the great advancements in the areas of carbon cycling, vegetation dynamics, and river routing. The major differences between CLM 2.0 and CLM initial version are: 1) the biome-type land cover classification scheme was replaced with a plant functio

15、nal type (PFT) representation with the specification of PFTs and leaf area index from satellite data; 2) the parameterizations for vegetation albedo and vertical burying of vegetation by snow; 3) canopy scaling, leaf physiology, and soil water limitations on photosynthesis to resolve deficiencies in

16、dicated by the coupling to a dynamic vegetation model; 4) vertical heterogeneity in soil texture was implemented to improve coupling with a dust emission model; 5) a river routing model was incorporated to improve the fresh water balance over oceans; 6) numerous modest changes were made to the param

17、eterizations to conform to the strict energy and water balance requirements of CCSM; 7) Further substantial software development was also required to meet coding standards. Besides the changes from a software engineering perspective, the differences between CLM3.0 and CLM2.0 are: 1) several improvem

18、ents to biogeophysical parameterizations to correct deficiencies; 2) stability terms were added to the formulation for 2-m air temperature to correct this; 3) the equation was modified to correct a discontinuity in the equation that relates the bulk density of newly fallen snow to atmospheric temper

19、ature; 4) a new formulation was implemented that provides for variable aerodynamic resistance with canopy density; 5) the vertical distribution of lake layers was modified to allow for more accurate computation of ground heat flux; 6) a fix was implemented for negative round-off level soil ice cause

20、d by sublimation; 7) a fix was implemented to correct roughness lengths for non-vegetated areas. Documentation for the Community Land Model (CLM3.0) was provided by Oleson et al. (2004). The simulations of CLM2.0 coupling with the Community Climate are described in Bonan et al. (2002). The simulatio

21、ns of CLM3.0 with the Community Climate System Model (CCSM3.0) are summarized in the Special Issue of Journal of Climate by Dickinson et al. (2005), Bonan and S. Levis (2005). Concurrent with the development of the Community Land Model, the CLM initial version was undergoing further development a

22、t Georgia Institute of Technology and Beijing Normal University in leaf temperature, photosynthesis and stomatal calculation. Big-leaf treatment by CLM initial version and CLM3.0 that treat a canopy as a single leaf tend to overestimate fluxes of CO2 and water vapor. Models that differentiate betwee

23、n sunlit and shaded leaves largely overcome these problems. A one-layered, two-big-leaf submodel for photosynthesis, stomatal conductance, leaf temperature, and energy fluxes was necessitated to the CLM initial version that is not in the CLM3.0. It includes 1) an improved two stream approximation mo

24、del of radiation transfer of the canopy, with attention to singularities in its solution and with separate integrations of radiation absorption by sunlit and shaded fractions of canopy; 2) a photosynthesis–stomatal conductance model for sunlit and shaded leaves separately, and for the simultaneous t

25、ransfers of CO2 and water vapor into and out of the leaf—leaf physiological properties (i.e., leaf nitrogen concentration, maximum potential electron transport rate, and hence photosynthetic capacity) vary throughout the plant canopy in response to the radiation–weight time-mean profile of photosynt

26、hetically active radiation (PAR), and the soil water limitation is applied to both maximum rates of leaf carbon uptake by Rubisco and electron transport, and the model scales up from leaf to canopy separately for all sunlit and shaded leaves; 3) a well-built quasi-Newton–Raphson method for simultane

27、ous solution of temperatures of the sunlit and shaded leaves. For avoiding confusion with the Community Land Model (CLM2.0, CLM3.0 versions), we name this improved version of the Common Land Model as CoLM. This was same as model now supported at NCAR. NCAR made extensive modifications mostly to m

28、ake more compatible with NCAR CCM but some for better back compatibility with previous work with NCAR LSM. For purpose of using in a variety of other GCMs and mesoscale models, this adds a layer of complexity that may be unnecessary. Thus we have continued testing further developments with CLM initi

29、al version. Some changes suggested by Land Model working groups of CCSM are also implemented, such as, stability terms to the formulation for 2-m air temperature, a new formulation for variable aerodynamic resistance with canopy density. CoLM is radically different from either CLM initial version or

30、 CLM2.0 or CLM3.0, the differences could be summarized as follows, 1) Two big leaf model for leaf temperatures, photosynthesis-stomatal resistance; 2) Two-stream approximation for canopy albedoes calculation with the solution for singularity point, and the calculations for radiation for the separ

31、ated canopy (sunlit and shaded); 3) New numerical scheme of iteration for leaf temperatures calculation; 4) New treatment for canopy interception with the consideration of the fraction of convection and large-scale precipitation; 5) Soil thermal and hydrological processes with the consideratio

32、n of the depth to bedrock; 6) Surface runoff and sub-surface runoff; 7) Rooting fraction and the water stress on transpiration; 8) Use a grass tile 2m height air temperature in place of an area average for matching the routine meteorological observation; 9) Perfect energy and water balance wi

33、thin every time-step; 10) A slab ocean-sea ice model; 11) Totally CoLM coding structure. The development of CoLM is trying to provide a version for public use and further development, and share the improvement contributed by many groups. The source code and datasets required to run the Co

34、LM in offline mode can be obtained via the web from: The CoLM distribution consists of three tar files: CoLM_src.tar.gz CoLM_src_mpi.tar.gz CoLM_dat.tar.gz. The file CoLM_src.tar.gz and CoLM_src_mpi.tar.gz contain code, scripts, the file CoLM_src.tar is the serial version of the CoLM,

35、and the file CoLM_src_mpi.tar.gz is the parallel version of the CoLM, the file CoLM_dat.tar contains raw data used to make the model surface data. The Table 1 lists the directory structure of the parallel version model. Table 1: Directory Name Description colm/rawdata/ "Raw" (highest provi

36、ded resolution) datasets used by CoLM to generate surface datasets at model resolution. We are currently providing 5 surface datasets with resolution 30 arc second: DEM-USGS.30s LWMASK-USGS.30s (not used) SOILCAT.30s SOILCATB.30s VEG-USGS.30s BEDROCKDEPTH (not available) LAI (not availa

37、ble) colm/data/ Atmospheric forcing variables suitable for running the model in offline mode colm/mksrfdata/ Routines for generating surface datasets colm/mkinidata/ Routines for generating initial datasets colm/main/ Routines for executing the time-loop calculation of soil temperatures, wat

38、er contents and surface fluxes colm/run/ Script to build and execute the model colm/graph/ GrADs & NCL files for display the history files colm/interp/ Temporal interpolation routines used for GSWP2 & PRINCETON atmospheric forcing dataset colm/tools/ Useful programs related with model runnin

39、g The scientific description of CoLM is given in [1]. Dai, Y., R.E. Dickinson, and Y.-P. Wang, 2004: A two-big-leaf model for canopy temperature, photosynthesis and stomatal conductance. Journal of Climate, 17: 2281-2299. [2]. Oleson K. W., Y. Dai, G. Bonan, M. Bosilovich, R. E. Dickinson,

40、 P. Dirmeyer, F. Hoffman, P. Houser, S. Levis, G. Niu, P. Thornton, M. Vertenstein, Z.-L. Yang, X. Zeng, 2004: Technical Description of the Community Land Model (CLM). NCAR/TN-461+STR. [3]. Dai, Y., X. Zeng, R. E. Dickinson, I. Baker, G. Bonan, M. Bosilovich, S. Denning, P. Dirmeyer, P. Houser, G.

41、Niu, K. Oleson, A. Schlosser, and Z.-L. Yang, 2003: The Common Land Model (CLM). Bull. of Amer. Meter. Soc., 84: 1013-1023. [4]. Dai, Y., X. Zeng, and R.E. Dickinson, 2002: The Common Land Model: Documentation and User’s Guide (http://climate.eas.gatech.edu/dickinson/). We value the responses a

42、nd experiences of our collaborators in using CoLM and encourage their feedback on problems in the current model formulation and the coding, as well as insight and suggestions for future model refinement and enhancement. It would be particularly helpful if users would communicate such feedback inform

43、ally and where possible share with us documented model applications including manuscripts, papers, procedures, or individual model development. 2. Creating and Running the Executable The CoLM model can run as a stand alone executable where atmospheric forcing data is periodically read in. I

44、t can also be run as part of the Atmosphere Model where communication between the atmospheric and land models occurs via subroutine calls or the special coupler. In this User’s Guide, we’ll focus on the parallel version CoLM, most of the scripts and setting of the serial version CoLM are similar to

45、the parallel version, and even more simple. offline mode In order to build and run the CoLM on offline mode, two sample scripts: jobclm.csh, jobclm_single.csh, and the corresponding Makefile files are provided in run and the source code directories respectively. The scripts, jobclm.csh and jo

46、bclm_single.csh, create a model executable, determine the necessary input datasets, construct the input model namelist. Users must edit these scripts appropriately(适当的) in order to build and run the executable for their particular requirements and in their particular environment. These scripts are p

47、rovided only as an example to aid the novice user in getting the CoLM up and running as quickly as possible. The script jobclm_single.csh used to do a single-point offline simulation experiment, can be run with minimal user modification, assuming the user resets several environment variables at the

48、top of the script. In particular, the user must set ROOTDIR to point to the full disk pathname of the model root directory. And the jobclm.csh is used to do a global or regional offline simulation experiment, usually should be modified heavily to fulfill different requirements. The following part we

49、’ll explain the jobclm.csh in detail. The script jobclm.csh can be divided into five sections: 1) Specification of script environment variables, creating header file define.h; 2) Compiling the surface data making, initial data making, time-loop calculation programs respectively. 3) Surface dat

50、a making, including input namelist creating; 4) Initial data making: including input namelist creating; 5) Time-loop calculation: including input namelist creating. 2.1 Specification of script environment variables The user will generally not need to modify the section of jobclm.csh, exce

51、pt to: 1) set the model domain edges and the basic computer architecture, 2) set the model path directory, 3) create the subdirectory for output, and 4) create the header file $CLM_INCDIR/define.h. BOX 1: EXAMPLE FOR SPECIFICATION OF SCRIPT ENVIRONMENT VARIABLES # set the basic comput

52、er architecture for the model running #setenv ARCH ibm setenv ARCH intel # set the model domain for north, east, south, west edges setenv EDGE_N 90. setenv EDGE_E 180. setenv EDGE_S -90. setenv EDGE_W -180. # set the number of grids of the CoLM and the forcing dataset at long

53、itude and latitude directions setenv NLON_CLM 360 setenv NLAT_CLM 180 setenv NLON_MET 360 setenv NLAT_MET 180 # set the number of processes used to parallel computing, MPI related. setenv TASKS 24 # The user has to modify the ROOTDIR to his/her root directory, for example, /people. s

54、etenv ROOTDIR /people/$LOGNAME # 1) set clm include directory root setenv CLM_INCDIR $ROOTDIR/colm/include # 2) set clm raw land data directory root setenv CLM_RAWDIR $ROOTDIR/colm/rawdata # 3) set clm surface data directory root setenv CLM_SRFDIR $ROOTDIR/colm/mksrfdata # 4) set clm

55、input data directory root setenv CLM_DATADIR $ROOTDIR/colm/data # 5) set clm initial directory root setenv CLM_INIDIR $ROOTDIR/colm/mkinidata # 6) set clm source directory root setenv CLM_SRCDIR $ROOTDIR/colm/main # 7) set executable directory setenv CLM_EXEDIR $ROOTDIR/colm/run # 8)

56、 create output directory setenv CLM_OUTDIR $ROOTDIR/colm/output mkdir -p $CLM_OUTDIR >/dev/null #------------------------------------------------------ # build define.h in ./include directory #------------------------------------------------------ \cat >! .tmp << EOF #undef coup_atmosmodel

57、 #undef RDGRID #undef SOILINI #define offline #undef BATS #undef SIB2 #undef IGBP #define USGS #define EcoDynamics #define LANDONLY #undef LAND_SEA #undef SINGLE_POINT #undef MAPMASK #define NCDATA #define PRINCETON #undef GSWP2 #undef DOWNSCALING #define WR_MONTHLY EOF

58、 if ($TASKS > 1) then \cat >> .tmp << EOF #define MPI EOF Endif \cmp -s .tmp $CLM_INCDIR/define.h || mv -f .tmp $CLM_INCDIR/define.h The ARCH variable is used to set the architecture of the model running, and in the following section of the jobclm.csh, the make command will use th

59、e ARCH variable to invoke different Makefile to compile the model. The EDGE_N, EDGE_E, EDGE_S, EDGE_W four variables are used to locate the model domain edges, especially on the model surface data making. The number of model grids at latitude or longitude direction is set by the NLAT_CLM and NLON_CL

60、M, these also are used for surface data making. The number of forcing dataset grids at latitude or longitude direction is set by the NLAT_MET and NLON_MET, these help do some simple forcing data downscaling when the model grids not exactly match the forcing dataset grids. The number of processors in

61、volved in the parallel computing is set by the TASKS environment variables, if TASKS is great than one, the MPI cpp token will be specified in define.h automatically, and the MPI parallel function will be build into the model, users could modify this logic according to your own requirements. The

62、file define.h contains model-dependent C-language cpp tokens. C-preprocessor directives of the form #include, #if defined, etc., are used in the model source code to enhance code portability and allow for the implementation of distinct blocks of functionality (such as incorporation of different mode

63、s) within a single file. Header file, define.h, is included with #include statements within the source code. When make command is invoked, the C preprocessor includes or excludes blocks of code depending on which cpp tokens have been defined in define.h. Table 2: define.h CPP tokens define.h c

64、pp token Description offline If defined, offline mode is invoked RDGRID If defined, the latitude and longitude of model grids are provided by input data USGS If defined, USGS 24 categories land cover legend are used IGBP If defined, IGBP 17 categories land cover legend are used SiB2 If de

65、fined, SiB2 11 categories land cover legend are used BATS If defined, BATS 19 categories land cover legend are used EcoDynamics If defined, dynamic vegetation model is activated LANDONLY If defined, only land grid are activated LAND_SEA If defined, land and sea grids are activated MAPMASK

66、If defined, users should supply the base map file to locate the specific region NCDATA If defined, netCDF format atmospheric forcing dataset being read, currently only supporting GSWP2 & PRINCETON datasets. PRINCETON If defined, the PRINCETON dataset being used. Depending on the NCDATA token. GSWP2 If defiend, the GSWP2 dataset being used. Depending on the NCDATA token. DOWNSCALING If defined, the simple downscaling method used