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South Asia Training Manual

1 Introduction Overview of User Interface
Introduction
Starting with version 4, APSIM comes with a user interface that lets users configure simulations using a drag and drop paradigm. This interface, unlike APSFront, provides complete access to all APSIM parameters and supports multiple point simulations.

Getting started
When first started (by clicking Windows Start Menu -> All Programs -> Apsim 7.3 r1387 -> APSIM User Interface), the interface shows a toolbar at the top, a toolbar at the bottom and two empty panes in between.

To create a simulation, click New on the toobar at the top of the screen and select a simulation that is closest

to the type of simulation you want to build.

This list of default simulations will be expanded over time. In fact, you can add your own default simulations to this list allowing you to reuse common simulations.

Description of a simulation

Simulation Configuration Tree

Properties for selected component (clock)

The tree control on the left shows the components that make up the APSIM simulation (Simulation Tree). Clicking on a component will show the properties for that component on the right. The picture above shows the clock component selected with it's properties on the right. It is recommended that users work their way from top to bottom in the simulation tree, checking each component's properties. Components can be renamed by selecting them, pausing for a second and then clicking again. Components may be deleted from the simulation tree by selecting the component and pressing delete. They can also be renamed or deleted by right mouse clicking on them and selecting "Rename" or "Delete". Remember though that deleting or renaming components usually has implications for other components. For example, deleting a crop usually means the management of that crop (e.g. sow, harvest etc), under the Manager component, needs to be changed as well. Note that you can change the order of components in the tree. You do this by right mouse clicking on the component and clicking Move Up or Move Down or you can hold down the Ctrl key and use the up and down arrow. The order of the components is not usually important it is merely cosmetic. The only exception is the order under the Manager folder component.

Adding components to a simulation via Toolboxes

To add components to a simulation tree, click the Standard button on the toolbar at the bottom of the window. This will show the standard toolbox containing many components and simulation entities that can be dragged onto the simulation tree.

A toolbox is a collection of reusable simulation components. By default there are many in the standard toolbox that cover a lot of the standard functionality required. The onus, though, is very much on the user to know which combinations of components work together. It is not expected that first time users will know which components work together. The recommendation is to start with a pre-built simulation and modify it, rather than starting from scratch. If in doubt, contact the APSIM Forum.

How to Build, Run and Graph a Simulation

Building, running and graphing simulations
Click on the New button and select a simulation that closest matches the simulation you're trying to create. For this example, choose Continuous Wheat Simulation.

Weather
The weather properties are located under the Met component in the simulation tree. There you will have the ability to browse to a weather file. Weather files need to be in APSIM format and should have a .met extension. Many sample weather files (e.g. Dalby) can be found in the apsim\met\sample directory under your apsim installation. e.g. c:\program files\Apsim73 r1387\apsim\met\sample Closely related to the weather file are the start and end date of simulation. These two properties can be found under the Clock component. They need to be within the range of the weather file. At this stage, to set the clock properties to include the entire climate record involves looking at the met file, taking note of the first and last date and entering those dates in the clock properties screen.

Soil
Picking a soil file involves finding a suitable soil from the Soils toolbox. To open the toolbox just click on the Soils button on the toolbar at the bottom of the window. The Soils toolbox has many soils to choose from.

Drag your chosen soil from the toolbox and drop into the paddock on the simulation tree. You can then delete

the existing soil in the paddock as it is no longer needed. Once the soil has been dropped it can be modified by clicking on it and then modifying the parameters to the right. Important: 1. Once you have dragged your soil onto your simulation tree, you should rename it to something with a shorter name. Some soil names in the toolbox are too long and will cause your run to crash if it is not renamed to something shorter. 2. It is important to remember that the soil must be parameterised for the crops that you're going to sow. If your simulation is going to sow wheat, then the soil must have LL, KL and XF values for wheat. These soil/crop values can be added to the soil but it is probably better to choose a soil that is already parameterised for the crops that you want.

The starting water that a simulation initialises with can be found by expanding the soil component in the simulation tree and then clicking Initial water.

The initial water can be specified in multiple ways by selecting one of the radio buttons and then entering a percent water or mm water. All changes made are automatically reflected in the graph on the right. Initial water can also be specified directly on a layer by layer basis. See the SW column in the Initial Nitrogen node.

nb. by entering a date in the Initial Nitrogen component you are able to specify a measured soil water and/or nitrogen at any date during the simulation. APSIM will reset the soilwater and/or nitrogen to these values on that date and keep going with its simulation. If you leave the date blank, APSIM will assign it the initial start date of the simulation. The starting nitrogen that a simulation initialises with can be found under the Initial Nitrogen node under the soil in the Simulation tree.

A single value for amount of nitrate or ammonia can be entered for the whole profile (in kg/ha)(by clicking in the respective "Total:" cells in the grid) OR amounts for individual layers can be entered in the grid.

Surface Residues / Organic Matter

The parameters for the initial surface residues can be found under the surface organic matter component in the simulation tree.

The "Organic Matter pool name" is simply an alphabetic description of the residue pool. The more important parameters are the "Organic matter type" and "Initial surface residue", "C:N ratio of initial residue" and the "Fraction of residue standing".

Fertiliser
This component does not have any editable parameters. This component only needs to be present if you are going to be doing fertiliser applications in your simulation.

Crops
Crops can be dragged from the Standard Toolbox and dropped onto a paddock. A crop can be deleted by selecting it and pressing Delete. Crops typically don't have any editable parameters. It is important to remember that the crop parameters LL (Lower Limit/Wilting Point), KL and XF (Both KL and XF are root growth parameters) come under the soil. This is because they are soil properties even though they depend upon the specific crop.

Simulation management
The Manager folder component contains all the management rules for the simulation. e.g. sowing fertilising irrigation tillage resetting of water and nitrogen

rotations

These rules can be dragged from the Standard toolbox (under Management folder in the Standard toolbox) and dropped under a Manager folder within a paddock.

The properties of the management rule can then be edited on the right. The management rule in the toolbox cover the same sort of functionality as the older APSFront software. It is also possible to drag an Operations Schedule component from the Standard toolbox and drop it on a paddock. This component lets you exactly specify your own manager operations for sowing, harvesting, etc. This will be familar to you if you have used control / parameter files in the past.

Reporting

APSIM is capable of producing an ASCII space separated output file containing whatever APSIM variables you want. In fact you need to exactly specify which variables you want output to the file. This is all configured from the Outputfile component. Variables Expand the outputfile component and click Variables

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The top pane allows you to enter some text to put at the top of the output file. This is usually used to put some constant values that you have used in your simulation. The bottom left pane lists which variables are to go into the output file (date, biomass yield etc) as columns. These variables can be deleted and reordered up and down in the same way as the components in the simulation. The bottom right pane gives you the variables that can be dragged onto the variable list in the left pane (adding them to the list; you can also double click them). The variables are grouped according to the components currently plugged into the simulation. To see the variables belonging to each component, simply choose the component from the "Component filter" drop down list. Some variables are layer variables or profile variables e.g.extractable soil water. Look for "Yes" or "No" in the Array? column to see if a variable is or not. These variables that are, when dropped onto the variable list will produce a number for each layer in the output file. If you want the sum of all layers, put a () in alongside the variable name in the Variable name column of the left pane. Other options include a (1-3) for the first 3 layers, or a (5) for the fifth layer. (click the ? button in the left pane for more information) Reporting Frequency The frequency of output is controlled by the Reporting Frequency sub component. The left pane contains a list of events. Whenever these specified events occur in the simulation, a line with the current values of the variables will be written to the output file.

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In the example above, a line of output will be produced every time the simulation harvests a crop. Just like with variables, use the "Component filter" drop down list on the right hand pane to see the events for each component that can be dragged to the left hand pane. If you want Daily output this can be achieved by dragging end_day event to the left had pane. The end_day event can be found by selecting the clock component from the drop down list in the right pane. APSIM is also capable of producing multiple output files. The user simply needs to drag and drop multiple outputfile components onto the simulation tree from the Standard toolbox (Or duplicate an existing outputfile). Each can then be configured independently. Precisely specifying outputs can quickly become tedious. If you frequently use common outputs, why not create a toolbox and drag your configured outputfile component and drop it onto your toolbox. You can then easily reuse this configured outputfile in your next simulation. To see how to do this, read the overview on toolboxes.

Multiple Simulations
Simulations can be saved to any folder by clicking the Save button. Likewise, running a simulation is as simple as clicking Run on the button bar. The user interface is capable of hosting multiple simulations within the single simulation tree. The example we've been working through here has a single simulation called Continuous Wheat. You can add another simulation by simply dragging this simulation and dropping it onto on the top level

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node Simulations - a copy will be made and there will be two simulations in the simulation tree.

Notice the second simulation called Continuous Wheat1 at the bottom. This simulation will be identical to the first simulation. Usually you would change a parameter in the second simulation to see what effect this parameter has on the result compared with the first simulation. Before you run the simulations the second simulation should be renamed to a more suitable name.

Running the Simulation(s)

Click the Run button on the toolbar at the top of your screen to run the simulation. Something to note is, if you have multiple simulations, and you only wish to run one of them, just click on the simulation that you wish to run so that it is highlighted like Continuous Wheat1 is in the image above. Then click the Run button. This will cause only the Continuous Wheat1 simulation to run. If you wish to run both simulations, just click on the very top simulations component to highlight it and then click the run button. This will cause all the simulations in your tree to be run. Often APSIM will produce a fatal error as a result of an invalid configuration or parameterisation. In this instance, it is important to consult the summary file that APSIM produces. Clicking on the summaryfile component will give quick access to the contents of this file. When looking for errors, always scroll down to the first error and fix that first.

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Once the simulation has sucessfully run just click on the outputfile component to see your output file. Note: The output file and summary files are just plain text files. As such the output files can be used as input for statistics software packages such as R, SYSTAT, MATLAB, GENSTAT etc. Also they can be opened in any text editor. After a run you will find the output files and summary files in the same folder that you have saved the simulation to. The user interface automatically names the output and summary file. It uses the simulation name in the tree (eg. Continuous Wheat Simulation) then adds the name of the output file (eg. outputfile)(nb. you are allowed to rename outputfile). The suffixes .out and .sum are used for the output and summary files respectively. This automatic naming ensures you can easily identify which output and summary files belong to which simulations.

Graphing the output and Exporting to Excel

If you do not already have a graph component in your simulation tree, then you can drag one there from the Graph toolbox. There are different types of graph components availible allowing you to choose the type of graph you wish to use. In the image below we have choosen an XY graph component.

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The graph component is able to find any output file on the same level or lower in the simulation tree. So dropping a graph component on the top Simulations node will allow it to find all the output files in all the simulations. Dropping on a specific simulation will allow it to find all the output files in the simulation and dropping it on a paddock will allow it to find all of them in that paddock. If you just drop it on a specific output file it will only be able to find that outputfile. To graph the output file, first fully expand the graph component by clicking the + symbol next to the graph component then work your way up from the bottom configuring each sub component. You can usually ignore the very bottom component ApsimFileReader . Then to view the graph all you have to do is click the graph component. Depending up the type of graph component it was, you will see that type of graph in the properties pane.

APSIM has a button on the main application toolbar to send the output file to Microsoft Excel.

To send an output file or multiple output files to Excel, just select them in the simulation tree and click the Excel button

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The help system

The button at the end of the main toolbar (at the top of the screen) gives quick access to the APSIM Documentation. A lot of documentation, including the science documentation and how some of the modules perform at different locations (i.e. sensibility tests), can be found under Module documentation. NOTE: The documentation you get when you click on this button is a copy saved to your hard drive that came when you installed APSIM. It is provided for when you do not have an internet connection. For a more up to date copy of the documentation please see the Documentation on our website (http://www.apsim.info/Wiki/APSIM-Documentation.ashx)

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Get started with South Asian data

On the workshop CD you'll see a folder called "Data", an online copy is Here. Copy this to your computer. The exercises below assume this will be "c:\apsim_workshop", though you can copy it to anywhere on your computer. Follow the instructions in Create your own or Add someone else's toolbox to add the toolbox "Rice_management.xml" (located in the Data directory above) to your APSIM User Interface. Don't point APSIM to the toolbox on the CD - use the copy stored on your local computer.

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2 Exercises Exercise 1: Fallow Water Balance

Fallow Water Balance
In this exercise you will explore the major elements of interest in soil water balance during a fallow - soil water storage, drainage, runoff, and evaporation. Changes will be examined over a one year period in the Bhola district of southern Bangladesh. The examples assume you have read and walked through the previous document: How to Build, Run and Graph a Simulation. 1. Create a new simulation using a blank simulation as a starting point 2. Choose a weather file for Bhola (c:\apsim_workshop\met_files\Bhola_1998-07.met) 3. Starting date: 1/1/2001 Ending date: 31/12/2001 4. Rename paddock node to field 5. Add a soil to the field node. A suitable soil characterised for the Bhola region would be : "North Joynags-06 No673. 6. From Soils toolbox, find and drag a Southern Bangladesh, Bhola district Silt, (Wheat PAWC = 138.5 mm, 1.5m) soil description onto the field node of the simulation tree, (located under Soils > Bangladesh > Southern Bangladesh > Bhola > Silt (North Joynags-06 No673)). Rename the soil to something shorter like Silt. 7. Set the starting water to 100% full - filled from the top. (expand the soil branch to see InitWater i.e. click the "+" next to Silt) 8. At the Initial nitrogen node, set the starting NO3 to 10 kg/ha (i.e. 6 and 4 in the 0-20 and 20-200 layers) and starting NH4 to 5 kg/ha (i.e. 4 and 1 in the two layers) 9. Add Surface organic Matter to the field: From Standard Toolbox Soil related, drag a Surface Organic Matter component onto the field node 10. Check that the default initial OM pool name is rice_stubble and OM type is rice and the mass is 0 kg/ha. (at "surface Organic matter" node) 11. From the standard Toolbox, drag a Outputfile onto the field node 12. Select the outputfile's Variables subcomponent. Choose these variables to report:
Component Clock Variable name dd/mm/yyyy as Date Year Day Met Silt Rain ESW - Extractable soil water (mm) ES - Evaporation Runoff DRAIN - Drainage NO3 - summed over profile (Do this by putting () next to the name in the "Variable name" column) eg. no3() (click "?" button next to variable list for more info) DLT_N_MIN - N mineralised - summed over profile

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SURFACEOM_WT - Weight of all surface organic materials. SURFACEOM_COVER - Fraction of ground covered by all surface organic materials.

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Surface organic matter

13. Select the "Outputfile" Reporting Frequency subcomponent. Delete "daily". Choose end_day reporting frequency for the output file. This can be found under the Clock component filter 14. Rename the simulation to something more meaningful: Silt Fallow 15. Save the simulation file as "c:\apsim_workshop\Fallow water balance.apsim" 16. Run the simulation by pressing the "Run" button at the top of the ApsimUI. 17. Create a graph of Date vs ESW. Hint: To do this, click on the Graph Toolbox at the bottom of the window to open the toolbox. Then drag in an XY component onto the output file in your simulation. Click on the "+" symbol next to XY component to expand the node. Click on the Plot component. In the Plot window click on the X variables square to make sure the background of the square is pink. Now click on the "Date" column heading. It should appear in the list in the square. Now click on the Y variables square to make its background pink. Click on the esw column heading. It will be added to the Y variables square. To have a clean line plotted with no points, under "Point type", choose "None". Now click on the XY component to view the graph. 18. Once you have created a chart it is possible to make modifications by adding new variables. It is also possible to mix the type of plots used on a graph. As an example, we will add rain as a bar chart on the Y2 axis. To do this, drag plot onto the XY node to create a duplicate, plot1. At plot1, remove esw and add rain as the y variable. To make the "rain" appear on the right hand axis, click rain in the square to highlight it, then "right" mouse click on it again. In the popup menu click on "Right Hand Axis". Select bar chart from "type" drop_down menu. Select XY node to see the line and bar chart combination. 19. Rename the XY graph node to Soil_water_storage The graph should show the ESW (in mm) increasing with day of year. The sudden increases are due to rainfall events and the declines to evaporation and drainage loss. The distribution of daily rainfall amounts helps see this more clearly.

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Note: You can also examine other components of the simulated soil water balance. 20. Drag Soil_water_storage to the outputfile node to make a copy of this graphics node. Rename the copy to Runoff_drainage 21. At the Plot1 node underneath the Runoff_drainage graph, remove rain from the Y variables box. Add runoff and drain to the Y variable box. Put both on the right hand axis (right click on the variable) to create a plot similar to the below figure.

Runoff occurs from the start of the monsoon season early in May-June, continuing through the wet season till Nov-Dec. Drainage begins sometime after the first runoff, once the soil profile is near full. (Remember, PAWC for wheat in this soil is 138.5 mm, so the profile is mostly in a saturated state whenever esw is above this limit).

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Additional exercise: You could also make a plot of soil evaporation. See if you can do this for yourself.

The effect of soil type on the water balance.

Runoff, es and drainage are affected by weather and soil water storage capacity. This simulation will add an additional soil and compare runoff from both soil types. The user interface still contains all the specifications provided for the previous simulation. If you drag the Silt Fallow node in the Simulation Tree to the top node Simulations, a copy of it will be made and your file will then have 2 simulations in it.

Notes:

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This second simulation can then be modified to add the characteristics of a second silt soil with higher water holding capacity. 1. From Soils toolbox, find and drag the Bangladesh -> Southern Bangladesh -> Patuakhali district -> "Silt (Shially-09 No783)" soil onto the paddock in the simulation tree and then remove the old soil (Hint: highligh the soil to delete and press the "Delete" key. It is important you drag in a new soil BEFORE you delete the old one, otherwise the simulation will lose all your soil reporting variables. Also remember to rename your soil to something shorter eg Silt_2 2. Since now we have a new soil we will need to go and set the initial soil water (InitWater) to 100% filled from top and initial soil nitrogen (Initial nitrogen) to NO3 to 10 kg/ha and NH4 to 5 kg/ha, as before. When you delete soils you also delete the initial soil water conditions and initial soil nitrogen conditions so these will need to be set similar to the conditions of the "Silt" soil. 3. Rename the simulation to "Silt2 Fallow". 4. Save the simulations. (C:\apsim_workshop\) 5. Run APSIM for the Silt2 soil simulation. 6. Graph both the output files by dragging an XY graph onto the top node Simulations in the simulation tree. By placing the XY graph under the "Simulations node", all output files in the simulation area will be available for plotting in this case, the Silt and Silt2 outputs. 7. Create a graph of date vs esw and runoff(cumulative, right hand axis). To make the runoff cumulative, it is the same procedure as to make the rain appear on the right hand axis. Only select "Cumulative" from the popup menu instead of "Right Hand Axis". Set "Point Type" to None. The figure below includes a plot of drainage for the 2 soils. See if you can also add drain as shown above to your esw-runoff plot. (Hint: create a plot1, do cumulative and right hand axis and choose "circles" under Point Type)

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The silt2 soil has only slightly higher runoff than the silt soil for all simulated events. Cumulative runoff for both is similar at over 1800mm. Is this what you might expect, given the PAWC of 33mm and the same rainfall and 100% full profiles as starting conditions? What can be seen from the accumulated drainage? Would runoff and drainage be the same if the initial PAWC for silt2 at the start had been different? (ie. Silt2 InitWater = 50%)

Notes:

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Notes:

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Additional exercise: explore the effect of changing curve number on the water balance. eg. for the silt2 soil, keep previous initial PAWC settings at 50% (Silt2) and change curve number from 94 to 84 in the Soilwat node. What is the effect on accumulated runoff and drainage?

Changes to the water balance by ponding water on the surface.

In the previous exercises we have investigated the APSIM water balance on free draining soils in accumulating stored soil water and in simulating effects of runoff, drainage and soil evaporation. The soil specified in the previous examples reflect a typical soil in a natural (cultivated or uncultivated) state unaffected by (farmer) imposed physical constraints to the flow of water in the landscape. Rice production particularly during the wetter months of the monsoon is grown under paddy conditions. The natural structure of the soil surface has been modified (puddled) to reduce drainage and bunding (ponding) imposed to reduce runoff. These conditions therefore require some change to parameters in APSIM to simulate the effect of ponded water above the soil surface. The following exercise will use the 'max_pond' parameter to enable ponding of surface water and modify 'KS' (hydraulic conductivity) values for each soil layer to restrict the rate of vertical drainage. 1. Drag Pond_depth on to the Manager Folder from "Rice Management Toolbox" -> "Rice" -> "Manager (Pond_depth)" 2. Change properties to: Name of your soil module: Silt Start date for ponding: 1-Jun (Start of wet season - bunds constructed) End date for ponding: 30-Oct (Crop maturing - open bunds) Maximum depth of pond: 150 Minimum depth of pond: 0

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Enable irrigation : No (set to No irrigation for the momemt) Start date for irrigation: 1-Jul End date for irrigation: 30-Oct Maximum number of irriagtions allowed: 0 3. Edit your soil file properties - Water - KS. (hydraulic conductivity in mm/day)to:
Component Depth 0-15 15-30 30-60 60-90 90-120 120-150 Variable name KS 1.0 1.0 24.0 24.0 24.0 24.0

4. Add additional report variables:

Component Met Soil Variable name rain DUL(1) sw(1) no3() drain runoff

5. Drag Irrigation on to the paddock field node in the "Silt Fallow Ponding" simulation from "Standard Toolbox" -> "Water Components (Irrigation)" 6. Run APSIM for the Silt Fallow Ponding simulation. 7. Create a graph of date vs DUL(1) and SW(1) (on Y axis) after deleting previous graphs. Rename this new graph to Ponding. 8. Create a second graph by dragging Ponding onto your outputfile. Select runoff and drain (Cumulative) on the Y axis. Rename this graph Drainage-Runoff.

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The Ponding graph shows the drained upper limit (DUL) of the first soil layer and volumetric soil water (sw(1)) in mm/mm for the first soil layer. Values above the DUL line indicate soil water over the drained upper limit and represent ponded water to a level as defined by "max_pond". The Drainage-Runoff graph presents simulated values for cumulative runoff (in excess of water stored by "max_pond") and cumulative drainage from the bottom of the profile as effected by "KS" input values.

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Additional exercise: Explore the effect of changing 'KS' rates (mm/day) on the level of cumulative runoff and drainage.

Notes:

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Exercise 2: Residue Cover Fallow

Tracking the decline of cover as residues decompose
APSIM simulates the influence of crop residues on the efficiency with which soil water is captured and retained during fallows. But residue cover declines as residues decompose. Residue decomposition is simulated in APSIM in response to weather, as well as the chemical composition of the residues and soil. By doing this simulation you will reinforce skills learned in previous exercises and learn to do some basic editing of default values to customise your simulations. The examples assume you have read and walked through the previous document: How to Build, Run and Graph a Simulation This simulation will demonstrate how surface residue decomposes over time. You should use the previous simulation as a starting point for this simulation. You need to add an initial amount of surface residues. 1. Reopen the previous file Fallow water balance.apsim. (Hint: c:\apsim_workshop\fallow water balance.apsim) 2. Save the file as Residue.apsim (Reminder: don't forget to use the Save as button, NOT the Save, or you will save these changes to Fallow water balance.apsim) 3. Remove the Silt2 Fallow simulation. We're going to use Silt Fallow as our starting point for this exercise. Also remove the graph components. Select the graph component and press "delete" or right click on the component and select Delete. 4. Make a copy of the Silt Fallow simulation by dragging to the top node in tree (Simulations). 5. Rename second simulation to Silt rice residue 6. Select the Surface Organic Matter node for editing: Set Organic Matter pool name: rice_stubble. Set Organic Matter type: rice. Set Initial surface residue: 2000 kg/ha. 7. Run the simulation 8. Create a graph of day vs surfaceom_cover and rain(right hand axis) for the Silt rice Residue simulation. Drag an XY graph from the "Graph toolbox" -> Graph -> "Graphs (XY)" onto the output file, and rename it to rice_cover. Remember to set "Point type" to None. To find out how to modify a graph see How To Modify a Graph Component

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It can be seen that periods of high decomposition rate match with higher rainfall and low decomposition with dry periods.

The effect of cover decline on runoff

In this activity, a comparison will be made between two simulations: Silt Fallow and Silt Rice Residue. 1. Drag the rice_cover graph that we've just created onto the simulations node at the top of the tree to create a copy. 2. Graph Date vs runoff(cumulative) 3. Rename this graph residues_runoff. Notice that data from both simulations (Silt Fallow and Silt rice residue) appears. 4. Drag grahic node Plot to residues_runoff node to create Plot1 5. Graph rain (this time select Type = Bar )

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The effect of residue type on speed of decomposition

The APSIM Surface Organic Matter model will decompose residues at differing rates according to the C:N ratio of the material, amongst other parameters. To demonstrate this we will reproduce the previous simulation but apply legume residues in the place of the rice straw residues. 1. Create another copy of the Silt rice Residue simulation and call it Silt cowpea residue. Delete the rice_cover graph 2. Select Surface Organic Matter for editing: Set Organic Matter pool name: cowpea_stubble. Set Organic Matter type: cowpea. Set Initial surface residue: 2000 kg/ha. set C:N ratio of initial residue: 20. (Remember you may want to change the Surface Organic Matter pool name to something like Cowpea as well) 3. Run this new simulation. (If you just select this simulation in the tree and click the run button it will only run this simulation instead of all of them. 4. Create a new graph for Silt rice residue and Silt cowpea residue simulations with residue cover as a function of time (eg date). Add rain to the right hand axis. 5. Rename the graph to "residue_type_cover".

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Notes:

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Exercise 3: Nitrogen cycling

Nitrogen cycling
In this exercise you will observe the fate of fertiliser nitrogen in a fallow situation: Urea to ammonium to nitrate and the loss of soil nitrate via denitrification. This simulation will introduce us to editing a simple Manager rule and to more advanced features of graphing simulation results. Firstly we need to set up our weather and soil data. The simulation is on silt soil in the Bhola region in Southern Bangladesh. The examples assume you have read and walked through the previous document: How to Build, Run and Graph a Simulation 1. Start with a new simulation based on Continuous Wheat 2. Change simulation name to Silt Fertilised 3. Save the file as N Fallow.apsim (C:\apsim_workshop\N fallow.apsim) 4. Choose a weather file for Bhola (c:\apsim_workshop\met_files\Bhola_1998-07.met) 5. Set the clock starting date: 1/1/2001 Ending date: 31/12/2001 6. Add a soil to the field node (North Joynags-06 No673) 7. From Soils toolbox, find and drag a Southern Bangladesh, Bhola district Silt, (Wheat PAWC = 138.5 mm, 1.5m) soil file ("Soils" > Bangladesh > Southern Bangladesh > Bhola > "Silt (North Joynags-06 No673)") onto the field node of the simulation tree. Remove the existing soil description after the addition. Rename the soil to something short like "Silt". If you like you can also reorder the soil component so it comes straight under the paddock. (Hint: Highlight your soil and use the Ctrl & up arrow to move a node up the tree) 8. Set the Starting water to 50% full, evenly distributed. 9. At the Initial nitrogen node, set the starting NO3 to 10 kg/ha (i.e. 6 and 4 in the 0-20 and 20-200 layers) and starting NH4 to 5 kg/ha (i.e. 4 and 1 in the two layers) 10. Set the initial surface organic matter to 2000 kg/ha wheat residues. 11. Remove the wheat component from the paddock, and all manager rules from the manager folder. 12. Drag a Fertilise on fixed date to your Manager component. ("Standard toolbox" -> "Management" -> "Manager (common tasks)" ) 13. Select Fertilise on a fixed date to edit: Enter fertiliser date: 15-Jan. Don't add fertiliser if N in top 2 layers exceeds: 1000. Module used to apply fertiliser: fertiliser. Amount of fertiliser to apply: 100.urea_N. 14. Make sure your simulation contains a Fertiliser component in your paddock. Even though it doesn't have any changeable properties it is still necessary when fertiliser is to be applied. 15. Select Outputfile Variables.

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16. Add the following variables to report:

Component Clock Variable name dd/mm/yyyy as Date Year Day Met Soil (Silt) Rain dlayer The thickness (in mm) of each soil layer esw Extractable Soil Water (mm) drain Drainage (mm) NO3() as NO3_Total Nitrate Nitrogen, summed over profile, aliased to NO3Total. (the as keyword creates an alias) NH4() as NH4_Total Ammonium Nitrogen, summed over profile, aliased to NH4Total UREA() DNIT() NO3 Nitrate Nitrogen, layered NH4 Ammonium Nitrogen, layered

17. Change reporting frequency (under Outputfile) to end_day. 18. Run the simulation 19. Create a graph of date vs urea, total ammonium and total nitrate. Drag an XY graph component onto the simulation. On the Plot node set "Point type" to None and leave "Type" as Solid line.

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Question: Why does the above graph look the way it does?

Illustrating the extent and conditions required for denitrification losses

Create a new chart of Date vs Rain, DNIT (right hand axis), ESW and NO3_Total.

From this chart you can see that some nitrogen is lost via denitrification when large amounts of nitrate is available in saturated soil conditions. But why do you think the level of denitrification is so low (0.1 kgN/ha/day) in this case?

Exploring vertical movement of nitrate, after fertilisation, through the soil profile
Let's look at the distribution of nitrate through the soil profile at the day fertiliser is applied and then at 1, 3 and 5 months after fertilisation. 1. Create a depth graph (from the graph toolbox), and expand all the sub-nodes. Go to the depth node, and select (so that they show a tick mark) the dates 15/01/2001, 15/02/2001, 15/4/2001 and 15/5/2001. Go to the Plot node and select NO3 as the X variables. Leave the Y variable as "Depth". Select the top graph node ("Depth"). Depth plots can only be done when the simulation has "dlayer" in the output file along with at least one other layered variable. This is why we included no3 and nh4 as layered variables in the output file and not just the summed variables for NO3() and NO4(). (Hint: adding () to an array variable like "NO3" to form "NO3()" will sum the nitrate values from all the soil layers)

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From this chart you can see the change (on the X axis) in the distribution of nitrate (NO3) in the soil profile (Y axis) over time in response to the addition of urea fertiliser and leaching processes at the start of the wet season. (The default title "Depth" can be changed to something more suitable ie. Change in soil NO3 over time Question: Why is there little change before the 15th of May? Repeat the steps above and create another graph this time selecting NH4.

Notes:

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Question: What has happened to the NH4? Try changing the dates to look at NH4 at 1, 5 and 10 days after fertiliser has been applied.

From this chart you can see the change in the distribution of NH4 in the profile occurs very rapidly over the course of a few days. NH4 is converted to NO3.

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Additional exercise: Try creating another simulation with clock set between 14/01/2001 and 31/01/2001. Create a time series graph of urea(), NO3_total and NH4_total in the profile over a period of 15 days after fertiliser is applied. Would the simulated process be the same if the fertiliser was applied in the middle of the wet season (August)?

Movement of Nitrogen between Organic Matter Pools

In this exercise we track the movement of nitrogen in fresh organic matter into soil microbial biomass and further into mineral nitrogen. We shall compare the flows in these processes for incorporation of two types of residues wheat and cowpea. 1. Make a copy of the Silt fertilised simulation by dragging to the top node in the tree (Simulations) 2. Delete all the XY and Depth graphs. - This setup already includes wheat residues on the surface at 2000 kg/ha and C:N ratio of 80 3. Change starting NO3-N to 60 kg/ha (36 and 24 in each of the 2 layers), leaving NH4-N at 5 kg/ha 4. Remove Fertilise on fixed date from your paddock component 5. Drag Tillage on fixed date to the Manager folder in your paddock component for this new simulation. (open "Standard toolbox" -> "Management" -> "Manager (common tasks)" ) 6. Change the Tillage management parameters to: date = 15-Jan Select Module used to apply the tillage as Surface organic matter or Wheat if renamed Change the Tillage type parameters to: type = tine Module used to apply the tillage = Surface Organic Matter Tillage Type = user_defined

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User defined depth of seedbed preparation = 100 (mm) User defined fraction of surface residues to incorporate = 1.0 7. Change simulation name to Silt wheat residues incorp. 8. Choose these variables to report:
Component Clock Soil (Silt) Variable name dd/mm/yyyy as Date Biom_n() as biom_n_Tot Fom_n() as fom_n_Tot NO3() as no3_Tot

9. Create a copy of the Sand wheat residue incorp simulation and call it Sand cowpea residue incorp. 10. Change the initial surface residue parameters to 2000 kg/ha of Cowpea (type) residue. Set the C:N ratio to 20. (Remember you may want to change the Organic Matter pool name to cowpea as well. Remember to reflect this change in Tillage on a fixed date - Module used to apply tillage) 11. Run the two simulations for residue incorporation. 12. Graph both residue incorporation simulations with fom_n_tot (left hand axis), no3_tot and biom_n_tot (right hand axis), and fom_n_tot. (Drag an XY graph onto the top node (simulations), open the ApsimReader node and point to the 2 output files)

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Inspect the change in fresh organic N in residues (fom_n) with time. Note: There is a steep increase in the first few days when tillage incorporates the surface residues and this material is passed onto the soilN modules as FOM. Soil "fom_n" for legume is higher than for wheat residues reflecting the differences in N content of the 2 materials as determined by the C:N ratios input to the model. Differences between wheat and legume dynamics in decomposition of FOM and its N content can be seen in the transfer of N into the microbial N pool (biom_n_tot), and the effects of this transfer on the net immobilisation/mineralisation of organic N from/to the soil nitrate pool. NO3 levels increase over time reflecting changes in fom_n and biom_n pools. Question: Would these rates of change increase during the wetter and warmer months?

Notes:

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Exercise 4: Single season rice crop

Single season rice crop
In this exercise we will simulate the biomass and yield of a direct-seeded rice crop using APSIM-ORYZA. You will learn a bit more about specifying a Manager template, execute more than one run in batch mode and use the simulator to do a what-if experiment with fertiliser rates and type. These skills can also be used to experiment with time of planting, rate of sowing and different irrigation rates. The examples assume you have read and walked through the previous document: How to Build, Run and Graph a Simulation 1. Start a fresh simulation using Oryza as a template 2. Select the first example Rice to use for this simulation (delete the second example:'Ponding simulation' for the moment) 3. Choose the Bhola_1998-07.met weather file 4. Set the clock starting date: 1/1/2001, Ending date: 31/12/2001 5. Add a soil to the field node ("North Joynags-06 No673) 6. From Soils toolbox, find and drag a Southern Bangladesh, Bhola district Silt, (Wheat PAWC = 138.5 mm, 1.5m) soil description onto the field node of the simulation tree, (located under Soils > Bangladesh > Southern Bangladesh > Bhola > Silt (North Joynags-06 No673)) removing the existing soil description after the addition. Rename the soil to something short like Silt. If you like you can also reorder the soil component so it comes straight under the field. 7. Set the Starting water to 100% full - filled from top. 8. Set the Starting nitrogen to 10 kg/ha of NO3 (as 6 and 4 in each layer, respectively) and 5 kg/ha (4 + 1) of NH4 9. Drag a Surface Organic Matter componet from Toolbox - Soil related onto your paddock. 10. Select the Surface Organic Matter component for editing: Organic Matter pool name: rice_stubble. Surface organic matter type: rice. Initial surface residues: 0. 11. In the Irrigation component set Automatic irrigation to off. 12. Drag a fertiliser component from the toolbox onto your paddock. (You may want to reorder components above the output file) 13. In the Manager component, delete the Rice sowing rule. Drag a Rice-Direct seeding component from the Rice Management Toolbox into the Manager. 14. Change the sowing rule to: set sowing window START to 1-Jul set sowing window END to 1-Jul set Cultivar to local set number of plants per seedbed to 180

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15. Choose these variables to report:

Component Clock Variable name dd/mm/yyyy as Date Year Day Soil (Silt) Rice ESW NO3() as no3_tot cropsta as crop_stage dae wagt as total_biomass wso as storage_organs wrr as rice_yield (Variable not in drop down) tnsoil as N_avail

16. Choose an "end_day" reporting frequency. 17. Rename the simulation to Direct_seeded_rice. 18. Save the simulation file as Rice single season.apsim (C:\apsim_workshop\Rice single season.apsim) 19. Run the Direct_seeded_rice simulation 20. Graph total_biomass and rice_yield with an XY graph with Date on the X axis. (Drag or Insert the XY graph on the top simulation node to plot output from both simulations)

This simulation demonstrates a local rice variety (direct seeded) grown under rainfed conditions during the monsoon. Simulated rough rice yield and biomass indicate a favourable season for rainfall. Investigate the rainfall during the growing season by reporting additional variables.

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21. Add additional report variables:

Component Met Soil (Silt) Variable name rain DUL(1) sw(1) no3() nh4() drain irrigation

Irrigation

22. Rerun simulation 23. Create a new graph by copying your XY chart onto the 'Outputfile'. Copy 'Plot' onto this XY Chart1 to create a second Plot1. For Plot select Y variables dul(1) and sw(1) (solid line and no points). For 'Plot1' select rain (right hand axis and type= Bar).

This graph shows volumetric soil water levels (sw(1) in mm/mm) in the top layer compared with the drained upper limit(DUL)in layer 1. Soil water in the surface layer is effected by soil evaporation (decline in SW(1) during the drier winter months of January to March) while surface water occurs only during the high rainfall period of the monsoon.

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Single season transplanted rice crop under ponded conditions

In this exercise we will simulate the growth and yield response of transplanted paddy rice. Apply fertiliser at defined stages in crop development and apply irrigaton as required to maintain adequate water levels in a paddy. 1. Make a copy of the simulation Direct_seeded_rice by dragging it to the Simulations node at the top of the simulation tree. 2. Rename this copy to Transplanted_paddy_rice. 3. Delete the Rice-Direct seeding manager from the Manager folder 4. Drag Pond_depth on to the Manager Folder (from "Rice Management Toolbox" -> Rice-> "Manager (Pond_depth)" 5. Change properties to: Name of your soil module: Silt Start date for ponding: 1-Jun (Start of wet season - bunds constructed) End date for ponding: 30-Oct (Crop maturing - open bunds) Maximum depth of pond: 150 Minimum depth of pond: 50 (Note: This is the trigger for irrigation to be applied) Enable irrigation : No (set to No irrigation for the momemt) Start date for irrigation: 1-Jul End date for irrigation: 30-Oct Maximum number of irrigations allowed: 6 6. Edit your soil file properties - Water - KS. (hydraulic conductivity in mm/day)to:
Component Depth 0-15 15-30 30-60 60-90 90-120 120-150 Variable name KS 24 24 24 24 24 1

7. Drag Rice-Transplant Aman on to the Manager Folder (from "Rice Management Toolbox" -> Rice-> "Manager (Rice-Transplant Aman)" 8. Change properties to: Enter sowing window START date: 1-Jul Enter sowing window END date: 1-Jul Duration of seedbed: 25 Number of plants on hills: 2 Fertiliser type: urea_N Amount of fertiliser at transplant: 30 9. Save the file 10. Drag Fertilise on growth stage on to the Manager Folder (from "Rice Management Toolbox" -> Rice-> "Manager (Fertilise on growth stage)" 11. Change properties to: Amount of fertiliser to apply: 40

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Fertiliser type: urea_N 12. Drag a Rice residue on to the Manager Folder (from "Rice Management Toolbox" -> Rice-> "Manager (Rice residue) 13. Change properties to: Select your module to apply tillage : Surface Organic Matter Tillage type: user_defined Depth of seedbed preparation: 0 Fraction to incorporate: 0.85 14. Run 'Transplanted_paddy_rice' simulation Create an XY graph of Biomass and rice yield (XY chart copied with this simulation from Direct_seeded_rice should be correct)

The graph shows daily biomass development from seedling establishment until day (25) of transplant (specified by "Duration of seedbed" in manager rules for sowing). Biomass is reduced due to transplant shock before developing total biomass at maturity. Grain fill starts in the second week in September and reaches full grain yield at physiological maturity in the last week of October.

Notes:

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Create a second XY graph using Plot by dragging it onto your 'Outputfile'. Graph dul(1) and sw(1) on the left axis with rainfall and drainage (Cumulative) on the right hand axis.

Notes:

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Exercise 5: Crop rotations

Two monsoon rice crops (TAus - TAman)
In this exercise you will simulate two rice crops grown during the monsoon period. TAus rice is transplanted at the start of the wet season in June and followed by the a TAman crop in late August. The examples assume you have read and walked through the previous document: How to Build, Run and Graph a Simulation 1. Open the previous simulation Rice single season as a template. (C:\APSIM_workshop\Rice single season.apsim) 2. Use "Save as" to create a copy of this file in the c:\APSIM_workshop\ directory. Name this simulation Rotations. 3. Make a copy of Transplanted_paddy_rice by dragging it onto the Simulations node. 4. Rename the copy to Rice-Rice. 5. Select the Micromet node in paddock and delete (this is not required in these exercises) 6. Select your soil (silt) for editing and change the starting soil water to 10% full (Evenly distributed) 7. Select the Manager -> Rice-Transplant Aman rule to edit: Enter sowing window START: 1-Aug. Enter sowing window END: 1-Aug. Cultivar: BR23. Duration of seedbed: 25. Number of plants on hills: 2. Number of hills: 25. Number of plants per seedbed: 1000. (Plants/m2) Fertilizer type: urea_N. Amount of fertilizer at transplant: 100. 8. Select the Manager -> 'Pond_depth' rule to edit: Name of your soil module: Silt. Start date of ponding: 15-Apr. End date of ponding: 30-Oct. Maximum depth of pond: 150. Minimum depth of pond: 50. Enable irrigation: yes. Start date for irrigation: 15-May. End date for irrigation: 30-Oct. Max number of irrigations: 6. 9. Select the Manager -> Rice-Transplant Aus rule to edit: Enter sowing window START: 15-Apr. Enter sowing window END: 15-Apr. Cultivar: BR3. Duration of seedbed: 30. Number of plants on hills: 2. Number of hills: 25. Number of plants per seedbead: 1000. Fertilizer type: urea_N. Amount of fertilizer at transplant: 30. 10. Run the Rice-Rice simulation. Graph date (X axis) vs total_biomass and rice_yield (Y axis). ( Hint: Use your XY Chart from the previous simulation) Change the 'title' of your graph by renaming your 'XY Chart' to a more siutable name. (Hint: TAus-TAman rice (biomass and yield))

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In the above simulation two rice varieties have been selected for their duration to maturity (Medium: BR23 ~119 DAE and Medium short: BR3 ~100 DAE) which enabled two rice crops to be planted during the wetter months of the local monsoon season. Selecting the appropriate variety (duration to maturity) is an important factor in constructing any crop rotation or cropping sequence and can effect the outcome of any long-term cropping sequence scenario. The previous simulations have only considered fixed sowing dates. Under dryland conditions the opportunity to sow a crop may rely on a rainfall event due to the unavailability of irrigation. A planting window (window of opportunity) can be defined in the manager with sowing triggered on meeting a specific condition such as rainfall (ie. 20mm over 3 days) or level of soil water (ie. ESW > 100mm).

Adding a dry season crop (ie. wheat) into the rotation

The previous example demonstrated a simple crop rotation or sequence of two wet season rice crops. In this exercise you will replace the early rice crop with a dry season crop (ie. wheat) sown into a full profile in mid November following the TAman rice harvest. 1. Make a copy of 'Rice-Rice' by dragging it onto the 'Simulations' node. 2. Rename the copy to Rice-wheat. 3. Select clock and change the start and end dates for the simulation: Start date: 1/06/2001 End date: 31/05/2002 4. Select the Manager -> Rice-Transplant Aus rule and delete: 5. Select the Manager -> Rice-Transplant Aman rule to edit: Enter sowing window START: 15-Jul. Enter sowing window END: 15-Jul. Cultivar: BR23. Duration of seedbed: 25. Number of plants on hills: 2. Number of hills: 25. Number of plants per seedbead: 1000.
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Fertilizer type: urea_N. Amount of fertilizer at transplant: 50. 6. From the "Standard Toolbox" select "Crops (wheat)" and drag onto the paddock node. (You may want to reorder wheat to below the rice component) 7. From the Standard Toolbox select "management" -> "Manager (common tasks)" -> (Sow using a variable rule) and drag onto the manager folder in your 'paddock'. 8. Select Manager folder -> Sow using a variable rule to edit: Enter sowing window START: 1-Dec. Enter sowing window END: 1-Dec. Must sow: yes. Enter name of crop: wheat. Enter sowing density: 100. Enter cultivar: 'prodip. Enter crop class: plant. Enter row spacing: 250. From the "Standard Toolbox" select "management" -> "Manager(common tasks)(Harvesting rule)" and drag onto the manager folder in your paddock. 9. Select 'Manager folder' -> 'Harvesting rule' to edit: Enter name of crop to harvest when ripe: wheat. 10. From the "Standard Toolbox" select "management" -> "Manager(common tasks)(Fertilise at sowing)" and drag onto the manager folder in your paddock. 11. Select Manager folder -> Fertilise at sowing to edit: On which module should the event come from: wheat. On which event: sowing. Module used to apply fertiliser: Fertiliser. Amount of starter fertiliser at sowing: 40. Sowing fertiliser type: urea_N. 12. From the 'Rice Management Toolbox' select 'Rice' -> 'Manager' -> (Fertilise and Irrigate rabi crop) and drag onto the manager folder in your 'paddock'. 13. Select 'Manager folder' -> 'Fertilise and Irrigate rabi crop' to edit: Crop type: wheat. DAS to apply fertiliser: 20. Module used to apply the fertiliser: Fertiliser. Amount of fertiliser to apply: 30. Fertiliser type: urea_N. Amount of irrigation to apply: 60 14. Add additional report variables:
Component Wheat Variable name biomass as wheat_biom yield as wheat_yield

15. Make a copy of Fertilise and Irrigate rabi crop by dragging it onto the Manager folder node. 16. Select Manager folder -> Fertilise and Irrigate rabi crop1 to edit: Change DAS to apply fertiliser: 40. Change amount of fertiliser to apply: 30. Fertiliser type: urea_N. Amount of irrigation to apply: 60 17. From the "Standard Toolbox" select "management" -> "Manager(common tasks)(Irrigate at sowing)" and drag onto the manager folder in your paddock. 18. Select Manager folder -> Irrigate at sowing to edit: The module the event come from: wheat. . Which event should irrigation be applied: sowing.

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Module used to apply irrigation: Irrigation. Amount of irrigation to apply: 60. 19. From the "Rice Management Toolbox" select "Rice" -> "Manager (Rabi residue)" and drag onto the manager folder in your "paddock". 20. Select "Manager folder" -> "Rabi residue" to edit: The module the event come from: wheat. On which event should tillage be done: harvesting. Module used to apply the tillage: Surface Organic Matter. Tillage type: user_defined. User_defined depth of seedbed preparation: 0. User_defined fraction of surface residue to incorporate: 0.8. 21. Run the Rice-wheat simulation. Graph date (X axis) vs total_biomass, rice_yield, wheat_yield and wheat_biom (Y axis). ( Hint: Use your XY Chart from the previous simulation and add the reporting variables selected for wheat) Change the 'title' of your graph by renaming your 'Chart' to a more siutable name. (Hint: TAman rice-wheat rotation)

The above examples introduced a crop rotation or cropping sequence where two crops (rice and wheat) are grown in series over a single season. The previous exercises have only considered a 12 month period. In the next exercise you will evaluate a long-term scenario based on the rice-wheat simulation that you have created. Long-term simulations require a much longer climate record. The Bhola_1998-07.met file contains daily records from 1998 to 2007 and enables simulation of this cropping sequence over 9 years.

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Long-term rice-wheat rotation

1. Make a copy of 'Rice-wheat' by dragging it onto the 'Simulations' node. 2. Rename the copy to Rice-wheat scenario. 3. Select clock and change the start and end dates for the simulation: Start date: 1/06/1998. End date: 31/05/2007. 4. Run the Rice-wheat scenario simulation. Evaluate the 'XY Chart' showing total biomass and yield of both wheat and rice. Change the 'title' of your graph by renaming your 'Chart' to a more siutable name. (Hint: TAman rice-wheat scenario)

The above graph is an example of a simple "rice-wheat" rotation where crops are sown on fixed planting dates. In the following example you will evaluate the introduction of an opportunity crop into this long-term rotation. Opportunity crops rely on a particular event occuring that would enable a crop to be planted. A simple example of an event is "rainfall". (ie. During a specified window of opportunity, did we get sufficient rainfall to enable a particular crop to be planted?)

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Add an opportunity crop (ie.mungbean) to a long-term rice-wheat rotation

1. Make a copy of 'Rice-wheat scenario' by dragging it onto the 'Simulations' node. 2. Rename the copy to Rice-wheat-mungbean opportunity. 3. From the 'Standard Toolbox' select 'Crops' -> 'mungbean' and drag onto the 'paddock' node. (You may want to reorder 'mungbean' to below the 'wheat' component) (Hint: Ctrl + up arrow) 4. Make a copy of your 'Sow using a variable rule' in the 'Manager folder' by dragging it onto the Manager folder node. Rename the copy to 'Sow mungbean'. 5. Select 'Sow mungbean' for editing: Enter sowing window START date: 20-Mar. Enter sowing window END date: 7-Apr. Must sow: No. Amount of rainfall: 20. Number of days of rainfall: 3. Enter minimum allowable available soil water: 0. Enter name of crop to sow: mungbean. Enter sowing density: 45. Enter sowing depth: 30. Enter cultivar: berken. Enter crop growth class: plant. Enter row spacing: 250. 6. Make a copy of your 'Harvesting rule' in the 'Manager folder' by dragging it onto the Manager folder node. Rename the copy to 'Harvesting mungbean'. 7. Select 'Harvesting mungbean' for editing: Enter name of crop to harvest: mungbean. 8. Change report variables:
Component Wheat Variable name biomass yield

9. Select the water node in your soil (Silt) for editing: Make a copy of wheat by dragging it onto the water node. 10. Rename this copy to mungbean and select for editing: Change "xf" values of 1 at 0-90 cm and 90-120cm and 120-150cm to 0. (This restricts potential rooting depth for mungbean to only 60cm) 11. Run the Rice-wheat-mungbean opportunity simulation. Graph date (X axis) vs rice_yield, wheat.yield and mungbean.yield (Y axis). Rename the graph to 'Ricewheat-mungbean opportunity' ( Hint: Edit the old XY Chart copied over from the previous simulation)

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Question: How many years do you get a planting opportunity to sow mungbean? The previous examples have demonstrated the process for constructing a simple cropping sequence or rotation (Rice-wheat) based on fixed sowing dates. The rice seedling nursery was sown on the 15th of July with transplanting occuring after 25 days. The wheat was sown on the 8th of December allowing time for the TAman rice harvest and well within the optimal planting window for wheat at "Bhola". Mungbean was included in this simulation as an example of an opportunity crop. The sowing criteria required 20mm of rainfall to occur over a 3 day period if the crop was to be sown. As the graph shows, these conditions only occurred in 5 of the 9 years. Additional exercise: Explore the effects of changing the "Sowing criteria" for mungbeans on the frequency of a successful mungbean crop.

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Exercise 6: System evaluation

A simple cropping sequence: biomass, nitrogen and water
In this exercise you will construct time series graphs to help in the evaluation and discussion of the following key components of a rice-wheat cropping system: 1. Total above ground biomass and grain production during the season for both rice and wheat crops. 2. Soil nitrogen dynamics in response to applied fertiliser on soil nitrogen availability. 3. Soil water and ponding dynamics in response to rainfall and applied irrigation.

1. Create a copy of the Rotations.apsim file and rename it to Rice-wheat system.apsim. (C:\apsim_workshop\Rotations.apsim) Load the new APSIM file into the ApsimUI. Remove all the additional simulations except for Rice-wheat by selecting a simulation node and pressing the Delete key. 2. Select the outputfile -> Variables subcomponent. Add additional variables to report:
Component Fertiliser Silt Rice Wheat Variable name fertiliser NH4() rlai as LAI(rice) wheat.lai as LAI(wheat)

3. Run the simulation.

TAman rice-wheat rotation: Simulated biomass and grain yield for a transplanted "Aman" rice - wheat

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cropping sequence.

4. Select XY Chart1 and rename to Nitrogen. 5. In the 'Plot' window in addition to the Y variables: no3(), NH4(1) and N_avail add nh4().

Nitrogen: Simulated soil nitrogen dynamics for a TAman rice - wheat cropping sequence.

6. Add an additional graph to your Outputfile node. In the Y variables add the following variables: dul(1)and sw(1) on the lefthand axis. On the righthand axis add: irrigation. Create an extra plot component by dragging a 'plot' (from "Graph Toolbox" -> Graph -> "GraphBits (Plot)" onto the 'Outputfile'. Add rain (Righthand axis) into the Y axis in 'Plot1'. Change the type to Bar and select a new colour. Rename this graph to Water.

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Water: Simulated period of ponding during the monsoon rice crop. Rainfall and irrigation events occuring over the rice - wheat cropping season.

7. Create a graph of Leaf Area Index (LAI) for the rice and wheat crops. Plot LAI(rice) and LAI(wheat) on the Y axis. Add a second 'Plot' component (Hint: See documentation above for the water graph on adding a plot component) with Y variables: total_biomass and wheat_biom (right axis). Rename this graph to LAI.

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LAI: Simulated Leaf Area Index (LAI) for rice and wheat. Plant biomass is also included. Notes:

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Exercise 7: Climate change projections

Climate Change projections in APSIM - response to changing CO2
Climate change and agriculture are interrelated processes, both of which take place on a global scale. Global warming is projected to have significant impacts on conditions affecting agriculture, including temperature, carbon dioxide, glacial run-off, precipitation and the interaction of these elements (http://en.wikipedia.org /wiki/Climate_change_and_agriculture). This exercise aims to explore the effects of climate change using a simple wheat cropping system. Firstly, the response of wheat to elevated CO2 is examined. For this simulation a climate control component needs to be included. In this analysis, you will look at seasonal changes in rainfall, evaporation, transpiration and crop yields. 1. Construct a long term wheat simulation at 'Dinajpur'- use the Rice-wheat simulation in your 'Rotations.apsim' file as a guide. (Hint: Make a copy of Rotations .apsim and rename it to Climate change.apsim.) Delete all the simulations except for the Rice-wheat simulation as this will become the template for the following exercises. 2. Rename the Rice-wheat simulation to Wheat-350ppm. 3. Select a new met file. Use the browse button to select the Dinajpur.met file from c:\APSIM_workshop \met_files\. 4. Select clock for editing: Select the start date: 1/01/1959 Select the end date: 31/12/2009 5. Drag a ClimateControl component on to the Wheat-350ppm simulation (from "Standard Toolbox" -> "Meteorological (ClimateControl"). 6. Select ClimateControl for editing: Enter window to START: 1-jan. Enter window END: 31-dec. Change in maximum temperature: 0. Change in minimum temperature: 0. Relative change in daily rainfall: 0. Relative change in daily radiation: 0. Atmospheric CO2 Concentration: 350. (Hint: you may want to move 'ClimateControl' to below the 'met' component. Use Ctrl + up arrow)

7. Remove all the manager logic used for the previous rice simulation. (Hint: Delete Rice-Transplant Aman, Pond_depth, Fertilise on growth stage, Rice residue.) 8. Drag a tracker component on to the Manager Folder (from "Standard Toolbox" -> "Management (tracker)"). 9. Add the following lines to the tracker component:
Tracker variables sum of rain on start_of_day from sowing to now as RainSinceSowing sum of ep on end_of_day from sowing to now as Transp sum of es on end_of_day from sowing to now as SoilEvap

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10. Choose these variables to report: (under Output node)

Component Clock Variable name dd/mm/yyyy as Date Year Day wheat.yield as wheat_yield wheat.biomass as wheat_biom ESW NO3() wheat.yield as wheat_yield wheat.biomass as wheat_biom rain RainSinceSowing Transp SoilEvap

wheat Soil (Silt) wheat met tracker

11. Change 'Reporting Frequency' to harvesting. (Hint: Select question mark to display examples for reporting frequency) 12. Delete existing XY charts under the 'Outputfile' node. 13. Make a linked simulation of 'Wheat-350ppm' and rename it to "Wheat-450ppm". There are several ways to make linked simulations: a) Right click and hold down on the source simulation and drag it to the top level (simulations) node. A popup menu appears when you let go, select the "Create Link Here" option. b) Select the source simulation with the left mouse button, hold the keyboards <alt> key down, and drag it to the top level (simulations) node. The advantage of linked simulations is that changes made to any component are made to all linked components. More details are in the section Using linkage to reduce simulation duplication. 14. Select the linked simulation 'Wheat-350ppm1' (in blue) and rename to 'Wheat-450ppm'. 15. Right click on the ClimateControl component and select 'unlink this node' from the drop down box. (The blue underlined link will change to black text) 16. Select the ClimateControl for editing: Change Atmospheric CO2 Concentration to 450. 17. Save and run both simulations. (Hint: select the 'Simulations' node at the top and then the run button to run both simulations at once) 18. Create a graph comparing wheat yields from each of the simulations . Drag a Probability Exceedence component on to the 'Simulations node' (from "Graph" -> Graphs-> "Probability Exceedence"). 19. Graph 'wheat_yield' (X axis) vs 'Probability' (Y axis). Rename the graph to 'Wheat response under climate change scenario

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In the above example a 'Probability of Exceedence' chart was selected to compare the probability of grain yields under different background concentrations of atmospheric CO2 (350 ppm and 450 ppm) using 50 years of daily climate data from Dinajpur in northern Bangladesh. The graph highlights a yield response by APSIM to an elevated CO2 level of 450 ppm. However, increasing levels of CO2 are only one aspect to be considered in any climate change scenario with the IPCC (2007) predicting significant increases in global temperatures over the next 50 to 100 years.

The next exercise builds on the previous example by creating two additional simulations. The first will consider current levels of CO2 at 350 ppm but with an increase in minimum temperature of 1.5 oC. The second will maintain an increase in minimum temperature in conjunction with an increase in CO2 to 450ppm.

Climate change response to an increase in minimum daily temperature

1. Make a linked simulation of Wheat-350ppm and name it Wheat-350ppm+2degC. 2. Select ClimateControl for editing and right click and "unlink this node". (The ClimateControl will change from underlined blue to black text) 3. Select ClimateControl for editing: Change in minimum temperature: 2. 4. Run this new simulation.

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The Wheat response under climate change scenario graph now includes the results of this latest simulation. Create an additional simulation based on 'Wheat-450ppm' using the steps above. Rename this new simulation to 'Wheat-450ppm+2degC'. 5. Run new simulation.

Notes:

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Question: How has increasing minimum temperature affected grain yield in relation to an increase in the level of CO2? Additional exercise: Explore the effects of increasing maximum temperature under this scenario. Changes in biomass and grain yield will have a direct effect on transpiration and soil evaporation. Create an additional graph from the 'Graph' toolbox or by copying 'Wheat response under climate change scenario'. Selecting both SoilEvap and Transp on the X axis for graphing.

Notes:

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Climate change response to rainfall

In this exercise you will investigate changes to wheat yield in response to modifying rainfall, temperature and CO2 by creating a simple experiment. This simulation experiment requires a control treatment (previous wheat simulation based on a CO2 concentration of 350 ppm) and a number of additional treatments: (1) Increasing CO2 to 450 ppm (2) Increasing minimum temperature by 2 oC (3) Decreasing rainfall by 10% 1. Drag a Folder component onto the 'Simulations' node (from "Standard Toolbox" -> "Structural (folder)"). 2. Rename this folder to Senario. 3. Make a copy the Wheat-350ppm simulation by dragging it on the Scenario folder. Rename this simualtion to Control. 4. Copy the Wheat-450ppm simualtion to the Scenario folder and rename it to C450 (CO2:450ppm). (Unlink the simulation by right clicking and selecting Unlink this node) 5. Create a copy of Wheat-450ppm+2degC. Rename this copy to C450+T2 (CO2:450ppm and minimum temperature + 2 oC). 6. Create a copy of C450+T2 by dragging it onto the Scenario node. Rename this simulation to C450+T2-R5 (CO2:450ppm and minimum temperature + 2oC and rainfall -10%). 7. Select the ClimateControl node in C450+T2-R10 for editing: Relative change in daily rainfall: -10. 8. Run all the simulations in the Scenario folder. (Hint: Highlight the 'Scenario' folder and press "Run" to run all simulations together)

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9. Create a box plot graph showing the results of each treatment. To do this, click on the Graph Toolbox at the bottom of the window to open the toolbox. Then drag a 'Box Plot' component (from "Graph" -> "Graphs (Box Plot)") and drop onto the Scenario node.

Hint: To change the Y axis right click on the chart and select Format Graph. Select Axes. For the 'Left Axis' untick Minimum and change value to 0. Close 'TeeChart editor.

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The "box plots" used in the above graph represent median wheat yield (dotted line) in response to applied treatments (based on 50 years of simulation). The solid section (25th and 75th percentiles) with whiskers representing the 10th and 90th percentiles.

Additional exercise: In the above scenario, decreasing rainfall (at CO2 levels of 450ppm) had only a small influence on median wheat yields due to available irrigation. In this example wheat is a dry season (Rabi) crop sown into high levels of soil water at the end of the monsoon with additional irrigation applied during the growing season. Access to available surface or ground water for irrigation under a declining rainfall climate change scenario may present a challenge for future agriculture. What would the effect of reducing the amount of applied irrigation or reducing starting soil moisture have on potential grain yield?

Notes:

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How To How To: Creating an APSIM met file using EXCEL

APSIM met files consist of a section name, which is always weather.met.weather, several constants consisting of name = value, followed by a headings line, a units line and then the data. Spacing in the file is not relevant. Comments can be inserted using the ! character. At a minimum three constants must be included in the file: latitude, tav and amp. The last two of these refer to the annual average ambient temperature and annual amplitude in mean monthly temperature. The met file must also have a year and day column (or date formatted as yyyy/mm/dd), solar radiation (MJ/m2), maximum temperature (oC), minimum temperature (oC) and rainfall. The column headings to use for these are year and day (or date), radn, maxt, mint, rain. Other constants or columns can be added to the file. These then become available to APSIM as variables that can be reportted or used in manager script. Example met file: weather.met.weather latitude = -33.78 (DECIMAL DEGREES) tav = 16.47 (oC) ! annual average ambient temperature amp = 13.71 (oC) ! annual amplitude in mean monthly temperature year day radn maxt mint rain () () (MJ/m^2) (oC) (oC) (mm) 1991 1 28.0 38.9 13.4 0.0 1991 2 24.5 37.3 17.3 15.1 To create one of these files in Microsoft EXCEL, open EXCEL and enter data into columns like this:

It is important that the column widths are a bit wider than the data in them. Notice in the figure the maxt column is wider than it needs to be. The next step is to save the file as a Formatted Text (Space delimited)(*.prn) file, giving it a .met file extension. It is recommended that you keep your toolboxes, met files etc in a folder not under the APSIM installation directory. Perhaps you could create a folder called c:/apsim_toolboxes for storing these types of
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files. Easy way to calculate the tav and amp constants

The software team provides a tool called TAV_AMP that will calculate these 2 constants and insert them into a met file. To download the tool goto: http://www.apsim.info/apsim/Downloads/tav_amp.exe Full instructions for using the tool can be found here: http://www.apsim.info/apsim/Products/tav_amp.pdf

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How To: Create your own or Add someone else's toolbox

Quite often you may find yourself parameterising components the same way over and over again in your simulations. The user interface allows you to easily reuse these components in many simulations via your own toolboxes. You can create your personal toolbox and then drag components or even entire simulations to it. Next time you want to create a simulation or a part of a simulation, you can then goto your toolbox and reuse entities that you've used before. Toolboxes can also allow you to save and reuse soils that you have created, although these should be kept in a seperate toolbox to your simulations. You can also add toolboxes that other people have created, allowing you to quickly and easily collaborate with colleagues.

Create your own toolbox To create a new empty toolbox, either for simulations or for soils, click the Options button on the toolbar

You will see the following window,

To create a new toolbox click the following link,

A Toolbox is just an xml file that you can save anywhere on your hard drive. In the following window select the

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location and name of the xml file.

NB. The name of the xml file is the name that will appear as the Name of the toolbox in the bottom of your APSIM User Interface. So it pays not to make it too long.

Add a toolbox

After creating a new toolbox you should see the following window.

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We now need to add this new toolbox to the Apsim User Interface. To do this just click the following link,

Just browse to the location of the xml file for the Toolbox and select OK.

Then OK in the "Options" window and the Toolbox will be added to your Apsim User Interface. See below,

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Add someone else's toolbox If someone has created/modified a whole bunch of soils for a particular country or region. Or have created a whole bunch of management rules etc., an easy way for them to share this with you is for them to simple give you their Apsim Toolbox.

Any toolboxes that you create can be shared with others by simply giving them a copy of the .xml or .soils file for the relavent toolbox. Once you have obtained a copy of the another persons .xml or .soils file it is a very simple process to add it to APSIM.

It is the exact same procedure as above for "Add a toolbox" except that you just browse to the location on your hard drive where you have saved the other persons .xml or .soils file that you wish to add.

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How To: Adding crop properties to a soil

It is important to remember that the soil must be parameterised for the crops that you're going to sow. If your simulation is going to sow wheat, then the soil must have LL, KL and XF values for wheat.

If the soil you wish to use does not have these values for the crop you desire, then you can add them. Start by clicking on the soil component in your simulation tree, make sure the Water node is expanded

Under the Water node, copy an existing crop back onto the Water node.

Then Rename the newly created crop to whatever crop you want to add eg. Canola (nb. It must match the name of the crop component that you are going to drag onto the simulation tree exactly).

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In the User Interface on the right hand side you should now see that your new crop has been added with default values filled in for LL, PAWC, KL and XF. (these values are the same as whatever crop you copied) (You may have to use the horizontal scroll bar along the bottom of the table to view your crop. The table is editable so you may change any of the values in the table. SO BE CAREFUL. (nb. PAWC is not editable becaue is is calculated from DUL - LL)

Once you have changed the values for LL, PAWC, KL and XF to what you want, you are done. You can now continue building the rest of your simulation or do a run.

Note, you can copy and paste these values from other crops by selecting all the cells you want to copy with the mouse, and then pressing "Ctrl + C" and then clicking on the top cell of the LL column for the new crop you have added, then pressing "Ctrl + V". OR by just right clicking and selecting Copy, Paste etc.

You can find out more about LL, PAWC, KL and XF in the Science Documentation for SoilWat or SWIM2.

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How To: Modify a Graph component and copying the graph or it's data
Modify a graph component

After you have dragged a graph component to the desired location in your simulation tree so that it can see the necessary output files your next task is to modify the graph component to plot your desired data.

1. You can expand the nodes of the graph component by clicking the "+" symbol next to it. This will reveal its child components. You should repeat this for each child until you have a fully expanded tree under the graph component.

Each different type of graph component is slightly different in what child components it has, but the general rule for configuring is to start at the bottom most child component and work your way back up towards the graph component.

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2. Starting at the bottom is usually an "ApsimFileReader" component. This just lists the .out files that it has found and lets you preview the data. Use the browse button to view other .out files it has found.

3. The "Plot" component is where you specify which columns from the .out file you want to plot. It also lets you specify what type of graph you would like to use (solid line, dashed line, bar etc.) and what you want to use to mark the individual points on the graph.

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4. To specify which column to use as the X axis, you click on the "X variables" square to make its background pink. Then you click on the column heading of the column you wish to add. You will then see the column name appear in the "X variables" square. To delete it, just click on it in the square and press the delete button on your keyboard. You add specify the Y axis columns just click on the "Y variable" square to highlight it pink and once again click on the column heading. If you wish to plot multiple columns on the same graph just keep on clicking more column headings.

5. If you are plotting multiple columns and you want to plot one of the columns on the Y2 axis instead of on the Y axis. You can just click on the name in the "Y variables" square and then right mouse click on it again. In the popup menu just click on "Right Hand Axis". In the same way if you wish a column to be the cumulative total of that column you do the exact same thing as to plot it on the Y2 column only instead you click on "Cumulative" in the popup menu.

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6. You can specify what type of graph and type of point markings you want to use by using the "Type" and "Point type" drop down lists respectively.

7. Finally, to view the graph just click on graph component in the simulation tree.

8. To give the graph a different label, simply rename the graph component (eg. from "XY" to "Shaun's Graph"). The name of the component is used as the label of the graph.

Copying the graph or it's data

1. Right mouse click on the graph and select either "Copy to clipboard" to copy the image, or "Copy data to clipboard" to copy the data that has been plotted. They can then be pasted just like any other windows application.

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Graphing in ApsimUI
Graphs in the UI are structured representations of data - the structure describing where the data is found, and how it is presented. The graph components are built by the same toolbox / Drag and Drop operations as any other component in the simulation, though graphs are updated when displayed - not after the "run simulation" button is pressed. The graph toolbox has 3 folders - commonly used graph types; individual components used to make a graph, and collections of complex graphs and associated reports. The graph types are: XY (or scatterplot) charts allow the user to plot 2 variables from a set of data on different axes (Scatter plot ) A Probability of Exceedance chart that displays a single set of data against its cumulative frequency A Cumulative Distribution Function (CDF) that uses a more formal definition of cumulative frequency A box plot where quantiles and extremes of a data set are shown as overlaid rectangles (Box plot 3 SOI Phase (Phases of the Southern Oscillation Index - described in Nature a dataset in ENSO like groups, A Depth plot that describes a layered dataset over a soil profile, A Predicted - Observed chart that adds regression statistics to an XY plot, A R graphics chart that uses the R statistical computing language to desribe a graph. )

) charts that categorise

Each of these graph types is a composite of "graph bits" - normal usage is to take one of the graph types, drop it onto your simulation, and customise the "bits" to present the data as you wish. By default, the graph uses whatever data it finds in its position in the simulation tree: if it's dropped on an outputfile component, it will use data from that outputfile; if it's in a paddock, it will use all outputfiles within that paddock, and if it's at the top level simulations node it will use all the output files in all the simulations. Basic instructions on modifying components of a simple graph are found How to Modify a Graph Component. You will see that CDF and probability charts are a variation of simple XY charts; with a GDProbability object between the data source (ApsimFileReader) and the plot reader. This object calculates the "probability" column that is used as one axis by the chart. The three SOI chart variants serve to break a dataset into 5 categories, one for each phase of the SOI: positive, rising, zero, negative and falling. Each category serves to create a set of analogues: years when the SOI in a particular month (chosen by the user) is the same. A more detailed description of the methodology can be read here????? Unlike timeseries (eg X(Date) vs Y) plots, depth plots are a way to look at the soil profile at an instant in time they present depth on the vertical axis, and a data variable on the horizontal. These are used to great effect when displaying water or nutrient contents. Static values (eg LL, DUL) can be plotted as a guide. The R graphics component simply calls R to run a script that hopefully leaves behind an image file that is displayed on the first tab. The second tab is where the user enters the script. The third tab displays any error messages from R as it runs the script.

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How To: Using linkage to reduce simulation duplication

The APSIM user interface has the ability to create shortcuts to simulation components in much the same way as Windows Explorer can create shortcuts. Whole simulations, parts of simulations or individual components can be linked to another comoponent. When a component is modified in one place, it is automatically updated in all linked copies.

To create a linked copy of a something, Drag the the thing you want to create a linked copy of using the right mouse button and drop it where you want the copy. Then select "Create link here" from the pop up menu.

There is no limit to the number of links that can be created, nor what can be linked.

Take the example were a base simulation has been created for a given scenario. If the intention is to then take this simulation and apply different fertiliser applications or sowing dates or soils to it, the tendancy would be to take a copy of the simulation and change the one attribute (e.g. fertiliser amount), doing this many times for each permutation. A problem then arises when the original simulation needs to be changed (e.g. a new variable added). This change then needs to be propogated through all the permutation simulations. Instead of creating a copy of the base simulation and changing the copy, the user can create a link to the base simulation. For the simulation example drag a copy of the simulation using the right mouse button and drop it on the parent node in the simulation tree and then select Create link here. This linked simulation is 'linked' to the base simulation. Changing the base simulation will change the linked version and vise versa. Once a linked copy has been created, the user can unlink the specific node that needs to be different to the base simulation. This can be done by right clicking on the linked node and selecting Unlink.

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This unlinked node can then be changed independently from the base node.

As another example, a folder could be added to the top level "Simulations" node where multiple soils could be dropped into a soil folder. These soils could then be linked into the simulations that needs them. e.g.

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How To: Submit a bug or feature request for APSIM

1. Go to www.apsim.info and click the "Bugs&Tasks" link at the top. 2. On the login page, just click the link called "Continue as "guest" without logging in". It is just below where you type your user name and password. 3. On the next page, you will see a list of all the bugs and feature requests that have been submitted to APSIM. Both by internal staff and external users such as yourself. It is suggested that you take a look at this list to see if someone else has already submitted the bug or feature request already. In the top left corner (as you look at it) click a link called "add a new bug" 4. This is the page that allows you to submit a bug or feature request. In the Description field just type a brief description, In the Project field choose which product your request is with regard to. In the Category choose what type of request it is. In Apsim Version just type in the version of APSIM that you noticed the bug in (if your request is not a bug then just leave it blank). Finally in the Comment box, write a detailed description of the bug or feature request. IMPORTANT leave your name and contact details (you don't have to but if you don't and we don't understand your request or we can not recreate the bug we will not be able to act on it).

5. When you are done, before you can create the bug you must first fill in the CAPTCHA. This is to stop automated hacking computer programs from entering fake bugs into our system.

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Then just click the Create button. Once this button is clicked you have sucessfully submitted your bug. 6. After submitting the bug you will be now taken to the update page for the bug you just submitted. You will see some links on the left hand side of the page (as you look at it). Most of these are irrelavent to you except for the "add attachment" link. You can click this to add any files or screen captures to do with your bug. You will also see your previously submitted comments underneath the Comment text box. If you want to add anything you may have forgotten to put, you can just type it in the Comment text box and click the Update button and it will be added to the bug.

If you click the "bugs" link at the top of the page, you will be taken back to the list of bugs page. You will notice that your bug has been added. If you click the link in the "desc" column, you will be taken back to this "update" page.

You can come back at any time and add more stuff about the bug. If you fix the bug yourself, or if you made a mistake and it wasn't really a bug, just log back in and you will be taken to the bugs page. Just click the link in the desc column for the bug you want to update to get to the update page for the bug and add a comment to the bug so we know not to worry about it. You can also add comments to any other bugs on the bugs page in exactly the same way. Not only the ones you have created.

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