CSMLite - The Simple Modular Crop Simulation Model Example

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CSMLite Project

oms3.prj.csm.zip

Invalid link [!/OMS FORTRAN Training/Slide3.PNG!]

The Figure above shows the conceptual structure of the CSMLite model.

• Components are shown in boxes, representing different states within the execution.
• Connecting arrows between the boxes represent data flow of some sort
  • Parameter settings
  • Data flow between components within a timestep
  • Data flow between components across a timestep

The Listing below (csm.sim) shows the OMS representation of the Data flow Figure as an executable simulation script.

/*
 * $Id: csm.sim 64915db25869 2011-10-23 23:38 -0600 Olaf David <odavid@colostate.edu> $
 *
 * Simulation file.
 */
sim(name:"CSM") {

    // for building from within the OMS Console
    build()

    // mostly for DLL/SO resources
    resource "$oms_prj/dist"

    // define output strategy: output base dir and
    // the strategy NUMBERED|SIMPLE|TIME
    //    outputstrategy(dir: "$oms_prj/output", scheme:SIMPLE)

    // run the model while the control component is not done.
    model (while:"control.notDone") {

        components {
            'control'       'csm.gen.Controller'    // model controller
            'input'         'csm.gen.Input_Init'    // input paramter from file
            'we'            'csm.gen.Weather_Rate'  // climate input
            'sw_rate'       'csm.gen.SW_Rate'       // SW rate
            'sw_integ'      'csm.gen.SW_Integ'      // SW integr
            'sw_outpt'      'csm.gen.SW_Outpt'      // SW ouput
            'pl_rate'       'csm.gen.Plant_Rate'    // plant rate
            'pl_integ'      'csm.gen.Plant_Integ'   // plant integration
            'pl_outpt'      'csm.gen.Plant_Outpt'   // plant output
        }
    
        connect {
            // control connect
            'control.doy' 'we sw_rate pl_rate \
                           sw_integ pl_integ \
                           sw_outpt pl_outpt'

            // weather input
            'we.srad' 'sw_rate sw_integ sw_outpt'
            'we.tmax' 'sw_rate sw_integ sw_outpt pl_rate pl_integ pl_outpt'
            'we.tmin' 'sw_rate sw_integ sw_outpt pl_rate pl_integ pl_outpt'
            'we.rain' 'sw_rate sw_integ sw_outpt'
            'we.par'  'pl_rate pl_integ pl_outpt'

            // input 
            'input.doyp'  'pl_rate pl_integ pl_outpt'

            // rate calculations
            'sw_rate.swfac1' 'pl_rate'
            'sw_rate.swfac2' 'pl_rate'
            
            // integration
            'pl_rate.lai' 'sw_integ'
            'sw_integ.swfac1' 'pl_integ'
            'sw_integ.swfac2' 'pl_integ'
            
            // output phase
            'pl_integ.lai' 'sw_outpt'
            'sw_outpt.swfac1' 'pl_outpt'
            'sw_outpt.swfac2' 'pl_outpt'
        }

        feedback {
             // carry lai into next day
            'pl_integ.lai'  'sw_rate'
        }
            
        parameter {
            // general
            'control.count'         3
            'input.simctrl'         "$oms_prj/data/SIMCTRL.INP"
            'we.simctrl'            "$oms_prj/data/WEATHER.INP"

            // soil water
            'sw_rate.soil_inp'      "$oms_prj/data/SOIL.INP"
            'sw_rate.irrig_inp'     "$oms_prj/data/IRRIG.INP"
            'sw_rate.sw_out'        "$oms_prj/output/sw.out"

            // plant
            'pl_rate.plant_inp'     "$oms_prj/data/PLANT.INP"
            'pl_rate.plant_out'     "$oms_prj/output/plant.out"
        }

        // optional logging 
        logging {
            'csm.Sw'        'OFF'
            'csm.Plant'     'OFF'
            'csm.Input'     'OFF'
            'csm.Weather'   'OFF'
        }
    }
}

EXERCISE 1 - Load the OMS CSMLite Modeling Project

Exercise Steps

1. Copy oms3.prj.csm to a directory of your choosing.
2. Start Netbeans and open this projects
3. Start the OMS Console and select this project

During this exercise we will review the contents of the projects, and review OMS relevant features in Netbeans.

Reference Section

• Getting Started - Netbeans and the OMS Console

EXERCISE 2 - Features of the OMS Console

1. Start the OMS Console and select the oms3.prj.csm project
2. Interact with the 17 buttons and features of the main console.
3. Go to the Parameter editor. The features of the editor will be explained. Explore the functionality of the tool.
4. Go to the Analysis Output Window. The features of this tool will be explained. Explore the functionality of the tool.

Reference Section

• Getting Started - Netbeans and the OMS Console

EXERCISE 3 - Study the CSMLite Components for OMS

1. Start Netbeans and open the oms3.prj.csm project.
2. Double click on the incomplete CSMLite component to bring up the source code in the edit window.
3. Study the component annotations, JNA-related syntax, and FORTRAN to C data type mapping as necessary.
4. Right click on the oms3.prj.csm to clean and build project. Examine and correct errors. When build is successful, check resulting output to the build and dist folders.

Reference Sections

• Creating FORTRAN Science Components
• OMS Annotation Reference

EXERCISE 4 - Use OMS DSL to Run a Unit Test of a CSMLite Component

1. Start OMS Console and select oms3.prj.csm project.
2. Open the incomplete unit test simulation file.
3. Complete the unit test simulation file.
4. Run the test simulation and examine results.

Reference Sections

• Creating FORTRAN Science Components
• OMS Annotation Reference

EXERCISE 5 - Use OMS DSL to Build and Run the CSMLite Model

1. Start the OMS Console and select the oms3.prj.csm project.
2. Open the incomplete simulation file (with .sim extension).
3. Complete the sub-elements in the simulation file
   1. Specify the output strategy
   2. Specify the components
   3. Connect the components
   4. Connect feedback components
   5. Add data input and parameters
   6. Compare the new simulation file to the completed counterpart.
4. Run the simulation and inspect output/error logs
5. Modify and add sub-elements in the simulation file at your discretion
   1. Change parameter values at your discretion
   2. Add more analysis elements to the simulation (optional)
6. Re-Run the simulation and inspect output/error logs

Reference Sections

• Building and Running a Model of FORTRAN Science Components in OMS
• OMS DSL Reference

EXERCISE 6 - Generate Model System Documentation Automatically

1. Start the OMS Console and open the oms3.prj.csm project
2. Select the CSMLite simulation
3. Click on the Auto-Doc button on the console toolbar and watch the output/error window to check progress.
4. Open and examine the CSMLite XML file in the output folder.
5. An instructor will open and display a PDF created from the XML file.

Reference Section

• Creating OMS Model System Documentation

EXERCISE 7 - Modify the CSMLite Model

Download

CSMLite with Plant2

oms3.prj.csm.zip

1. Start Netbeans and open the oms3.prj.csm project.
2. Open the Plant2 source code file.
3. Annotate and modify to make OMS compatible
4. Compare to completed OMS compatible source code file
5. Right click on oms3.prj.csm to clean and build project
6. Check contents of build and dist folders
7. Start OMS Console and select oms3.prj.csm
8. Open new simulation
9. Copy contents of previous basic simulation to new simulation
10. Modify components, connect, and feedback sub-elements to incorporate replacement component.
11. Run new simulation and check output/error logs

Reference Sections

• Creating OMS Fortran Science Components
• Building and Running a Model of FORTRAN Science Components in OMS
• OMS Annotation Reference
• OMS DSL Reference

EXERCISE 8 - Consider Options for Data Input and Output Management

1. Start the OMS Console and select oms3.prj.csm project
2. Engage in facilitated discussion to examine data I/O management on the OMS Java side visavis on the FORTRAN side.

Reference Section

• Provisioning Data to OMS Models (Data Input/Output)

EXERCISE 9 - Use OMS DSL to Calibrate a Model

Exercise Steps

1. Start the OMS Console and select either oms3.prj.csm or oms3.prj.prms.
2. Open a Luca simuation.
3. Run the simulation and view results
4. Make changes to the elements and sub-elements
5. Re-run the simulation and view results

Reference Sections

• Building and Running a Model of FORTRAN Science Components in OMS
• OMS DSL Reference

CSMLite Model Source Code, Simulation, and Data Files

CSMLite Source Code

Main

Weather

Soil-Water Availability

Plant Growth

Alternative Plant Component

Adjusted Simulation Control Data Input File

Adjusted FORTRAN Main

CSMLite OMS Simulation Files