Basic GAPS

A tool for investigating the dynamic and complex systems of the global environment.

 

GLOBE Program

Soil Characterization Team

 

 

                                               

 

 

 

 

 

 

 

Copyright ã Cornell Research Foundation, Inc. All rights reserved.

 

 

Contact Information

 

 

Jeff Melkonian                                              Jessica Robin

1123 Bradfield Hall                                                 Code 923

Cornell University                                        NASA Goddard Space Flight Center

Ithaca, NY 14853                                         Greenbelt, MD 20771

USA                                                                USA

Phone: (607) 227-9172                              Phone: (301) 614-6636

Fax: (607) 255-2106                                   Fax: (301)614-6695

Email: jjm11@cornell.edu                         Email: jrobin@ltpmail.gsfc.nasa.gov

 

 

 

Table of Contents                        Page

 

1       Welcome                                                                           6

         Sample Input and Output Data                                                    

 

2       Basic GAPS in Excel: System Requirements                     9

 

3       Introduction to Modeling and Basic GAPS Model              10

         Overview of Modeling

The Basic GAPS model

 

4       Summary of GLOBE data required for Basic GAPS          14    

 

5       Summary Instructions for Running Basic GAPS                15

 

6       Basic GAPS Excel Workbook: The ‘User Interface’ 17          worksheet

        

7       Basic GAPS Model Inputs                                                  19

            Instructions for downloading GLOBE data, entering

            downloaded data into the Basic

            GAPS input worksheets (‘ClimateInput’, ‘SoilInput’), and detailed

            descriptions of the ‘ClimateInput’            and ‘Soilinput’ worksheets

 

                        Soils Data

                                    Downloading GLOBE soils data from the

                                    GLOBE website

 

                                    Entering soils data into the ‘SoilInput’

                                    worksheet

 

                                    ‘SoilInput’ Worksheet: List of Inputs

 

                        Climate Data

 

                                    Downloading GLOBE climate data from the

                                    GLOBE website

                                               

                                                Data from one school

                                               

                                                Searching for missing data from nearby

                                                GLOBE schools

                                               

                                                Searching for missing data from nearby

                                                non-GLOBE sites

                                               

                                                Searching for data by latitude and longitude

                                               

                                                Searching for data by distance

 

                                    Entering climate data into the ‘ClimateInput’

                                    worksheet

 

                                    ‘ClimateInput’ Worksheet: List of Inputs

 

                        Phenology and Land Cover Data

 

                                    Downloading GLOBE phenology and land cover

                                    data from the GLOBE website

 

                                    Entering phenology and land cover data into

                                    the ‘ClimateInput’ worksheet

                       

                                    ‘ClimateInput’ Worksheet: List of Inputs

 

8       Running Basic GAPS                                                         41

 

9       Basic GAPS Model Output                                                 42

                  “View Table”

                        “View Graphs”

                                    Dynamic Graphs

                                    Static Graphs

 

10     Suggested Learning Activities                                           48

                  Impact of vegetation on soil water balance

                        Importance of soil characterization and soil texture

                        Impacts of global climate change

 

Appendix A                  Glossary                                                          50

 

Appendix B                  Request for participation in GLOBE data collection                              for the data required by Basic GAPS               53

 

Appendix C         Copyright license agreement                                    57

 

 

 

 

 

 

List of Figures

 

Figure                          Description                                             Page

 

1                Global Biomes                                                                                 7

2                 Basic GAPS user interface (‘User Interface’ Worksheet)        18

 

3A           Input dialog box for entering soils data                                       22

                   (‘SoilInput worksheet)

 

3B           Message box requesting if user has inputs for the                  23

                        runoff simulation (‘SoilInput’ worksheet)

 

3C              Message box for entering inputs required by the                      24

                        runoff simulation

 

4                 Sample ‘SoilInput’ worksheet with the soils inputs                 25

                        necessary for a Basic GAPS simulation

 

5                 Input dialog box for entering phenology and land cover data 38

                        (‘ClimateInput’) worksheet

 

6                 Sample ‘ClimateInput’ worksheet with the climate,                 39

                        phenology and land cover data necessary for a Basic GAPS

                        simulation

 

7A              Sample output from a Basic GAPS simulation                         43

                        (‘Output’ worksheet)

 

7B              Sample output from a Basic GAPS simulation                         43

                        (‘Output’ worksheet)

 

7C              Sample output from a Basic GAPS simulation                         43

                        (‘Output’ worksheet)

 

7D              Sample output from a Basic GAPS simulation                         43

                        (‘Output’ worksheet)

 

8                 Dialog box for selecting graphs of Basic GAPS            output             46
Basic GAPS Manual, Version 1

 

1       Welcome for Teachers

 

Basic GAPS is a computer model for students that can simulate the cycles of water and energy between the atmosphere, soil, and vegetation. Students can easily obtain the required soil, vegetation, phenology, and climate data from sources such as the GLOBE program data archive and input the information through guided menus. Once the model simulation runs, the change in soil water content, evaporation, transpiration and other environmental parameters can be displayed so that students can observe how different parts of the system change and are affected by each other.

 

A major goal of the Basic GAPS model is to teach students that the Earth's ecosystems are the result of closely linked, dynamic interactions among many processes and many components. Basic GAPS enables students to study the interplay among these processes in a quantitative way. They can examine linkages within a particular biome, such as the sensitivity of soil moisture to seasonal changes in the overlying vegetation or the amount of evaporation and transpiration under certain types of soil or land use. Using Basic GAPS, students can also make up different scenarios (such as increasing the temperature, changing the pattern of precipitation, or modifying the soil properties or vegetation type) to make predictions about how the ecosystem may respond. In this way, students, just like scientists, can pose and address questions regarding the impact of climate, including global climate change, on the environment.

Schools that would like to use Basic GAPS do not have to collect all the required input data themselves. In fact, all the input data required for Basic GAPS is available from the GLOBE student data archive. In this way, students can use either their own data or data from GLOBE schools from all over the world to explore many interesting regional or global environmental questions using Basic GAPS. Figure 1 shows an example of the major biomes of the world each of which have data collected by GLOBE students.

 

                  Figure 1. GLOBAL BIOMES. (Please note that, in MS Word,                                                 you can increase the size of this figure and the following                                            figures using the zoom button on the tool bar above or by                                       selecting ‘zoom’ under the ‘View’ pull down menu.)

 

 

 

We would, however, like to encourage schools that are interested in collecting data at their own sites to collect the whole range of measurements that are required for the Basic GAPS model (see Chapter 4: Summary of GLOBE data required for Basic GAPS). As more and more schools gather this information, we (GLOBE scientists and students) can work more closely together to explore important scientific questions related to the interaction of soils, vegetation and climate across the Earth’s biomes. At the present time, Scientists from the GLOBE Soil Characterization Team at Cornell University and NASA are looking for schools to work with us to develop GAPS study sites all over the world. Working together, we will use the data collected with the GAPS model to understand more about the Earth’s ecosystems and publish in scientific journals. We hope that you too will become part of this important project! Please look at Appendix C for more information on this, or contact us directly (Appendix B).

 

 

 

 

Sample Input (and Output) data

 

In order to work with Basic GAPS without downloading data, we have included sample soil, climate, phenology, and land cover input data with the Basic GAPS software. These are located on the worksheets labeled ‘SoilInput Example’ and ‘ClimateInput Example’. These data can be copied and pasted into the ‘SoilInput’ and ‘ClimateInput’ worksheets if you would like to try out the Basic GAPS model right away. Output from a model run using these data is shown in the ‘Output Example’ worksheet. This is meant to allow you to become familiar with the operation of Basic GAPS before you begin to enter and download your own data. Note that you can edit these data if you like (e.g. increasing or decreasing temperatures or precipitation) in order to explore how the model works.

 

2       Basic GAPS in Excel: System Requirements

 

Basic GAPS is written in a programming language called Visual Basic for Applications or VBA, and is used in Microsoft Excel. Basic GAPS was developed in Excel 2002 and has not been tested on earlier versions of Excel. If you have problems running the model on an earlier version of Excel, please contact us (Appendix B) and we will work with you to get the model running. We assume that the user has some experience with Excel; however it is by no means necessary that you be an ‘expert’ at Excel in order to use Basic GAPS.

 

VBA in Excel means that the model user interface, the model inputs, and the model outputs (graphs and tables) are separate worksheets in an Excel workbook (called ‘Basic GAPS’). The code for the input and output data, and for the model algorithms, was written in the VBA editor and lies “behind” the Excel worksheets. This code constitutes a VBA “Project” with structures for developing the user interfaces that you will use to enter data, run the model and examine model output. The basic approach of VBA is the manipulation of “objects” such as worksheets and cells in worksheets. This manipulation is accomplished by writing VBA code.

 

3       Introduction to Modeling and Basic GAPS

 

Basic GAPS is a dynamic, deterministic simulation model of the “soil-plant-atmosphere” system. The model describes, among other things, water uptake by plants, water and heat flux in soil, and the impact of climate on these processes.

 

What exactly is a dynamic, deterministic simulation model to a scientist?

 

When scientists talk about models, they are referring to a representation of a natural system such as the Earth’s climate or soils. This representation or model is developed using the best knowledge available to scientists and is often expressed as a set of mathematical equations that describe individual processes such as water uptake by plants. These equations are linked together, usually with a computer program. These linked equations are what we refer to as a simulation model. A simulation model is dynamic if it predicts how processes change over time (e.g. hourly, daily, monthly). Each model simulation has input parameters that describe what the natural system (e.g. soil properties, vegetation type) looks like at the beginning of the simulation. Other inputs are used as “drivers”, such as daily rainfall and temperatures, which constrain the model to certain conditions. The simulation model is then set to run with this input information until a set time limit is reached. At that time, the original properties of the system have changed based on the equations in the model and the drivers. Changes in the original properties constitute the output of the model and are analyzed by scientists. Basic GAPS is a particular type of dynamic simulation model called a deterministic simulation model. Basic GAPS is a deterministic model because it makes definite predictions about the changes in the properties of the natural system such as: “on Sept. 1, soil volumetric water content increased from 0.20 m³ m^-3 to 0.25 m³ m^-3”.

 

Why do scientists construct simulation models and what do they use the models for?

 

Scientists construct simulation models for several different reasons. Most often, scientists use models to help in their research. Models provide a quantitative description of a particular system and allow scientists to test theories of how that system operates. Used cautiously, models can provide scientists with the capability to make predictions of future conditions and direct our research efforts in areas that require further investigation. For example, models are often used to help design better experiments by identifying the parts of a system that have the largest impact on something that is an output from that system. For example, a scientist may ask how air and soil temperature will affect bud burst timing. Models are available to help the scientist try out different possible scenarios that might occur before testing them in a field experiment. Results from these experiments can, in turn, be used to improve the model.

 

Scientists also use models to study large, complex systems such as soils and climate. Models integrate the different parts of these systems so that the scientists can examine the behavior of the system as a whole. This is exactly what both GLOBE scientists and, with Basic GAPS, students can begin to do. Models like GAPS are designed specifically for scientists and students to better understand the impact of these interactions on the environment.

 

The Basic GAPS model

 

GAPS stands for General-Purpose Atmosphere-Plant-Soil Simulator. Professor Susan Riha at Cornell University, Ithaca, NY, USA, the GLOBE Co-Principal Investigator for Soil Characterization, and graduate students and staff members in her research program developed this model. GAPS has been used by a large number of scientists in many different research applications. GAPS uses climate, soils and plant inputs to describe soil and plant responses to changes in climate. GAPS represents soil, plant and atmospheric processes in several different ways so that the person using GAPS can select those processes that best fit with the input data and the purposes for which GAPS is being used. Basic GAPS is a student version of GAPS that contains the soil, plant and atmospheric processes that best fit with data like that collected by GLOBE students.

 

Both GAPS and Basic GAPS are “systems” models. They mathematically describe Earth system processes and components that are also represented in the GLOBE program: soil, atmosphere, hydrology, phenology and land cover. Both models can be used to predict how these processes and components will change under varying conditions. A critical attribute of these models, emphasized throughout this manual, is the capacity to link these components and processes. This allows us to examine the interactions among them that are so important to life on Earth. These include key components of the hydrologic cycle such as the relationship between precipitation, water flux from plants and soils, and runoff and drainage to ground- and surface water resources. Using models like GAPS and Basic GAPS, we can determine such things as how different soils and land covers can affect these key hydrologic cycle components.

 

The GAPS processes that we have included in Basic GAPS are:

 

·      Potential and actual water vapor loss from soil and vegetation surfaces. Potential water vapor loss or “potential evaporation” directly from soil surfaces (PotEvap) and from vegetated surfaces through stomata (pores on the leaves of plants) or “potential transpiration” (PT) is usually referred to as “potential evapotranspiration” or PET. These losses are considered “potential” losses because they represent the maximum evaporation that can occur when the soil surface is completely wet and when stomata are fully open. As the soil dries out due to water losses to the atmosphere, there is less soil water available for evaporation or plant uptake and the rates of both evaporation and transpiration decrease below their potential values. When this occurs, these are referred to as “actual evaporation” (ActEvap) and “actual transpiration” (ActTrans). There are several ways to calculate PET. In Basic GAPS, PET is calculated from mean daily air temperature, mean daily dew point temperature (minimum daily temperature is used as an approximation), elevation and latitude.

 

• ·      Plant water uptake. This variable is restricted to those sites that are partially or completely vegetated and to the times of year between green-up and green-down (see GLOBE Phenology protocols) when plants are capable of taking up water and transpiring it to the atmosphere. Plant water uptake is largely determined by PET and the plant-available water in the soil where there are roots present. When soil water is low, plant water uptake is reduced leading to the reductions in PT to ActTrans and, as the soil surface layer dries out, PotEvap to ActEvap as described above.

 

• ·      Soil water flow. Precipitation is used to “refill” the soil when the soil is dry which is when the amount of water in the soil is below its maximum capacity to hold water. The precipitation, or water, enters the first layer or horizon of soil (defined in the Soil Input section below). If more water enters than the” water holding” capacity of that horizon can hold, the water is transferred to the next horizon. This process is repeated from horizon to horizon. Any water moving out of the bottom horizon (after all horizons are at their water holding capacity) is referred to as “drainage”. This is a particularly important variable for soil scientists, hydrologists and environmental scientists because of its importance for maintaining water flow into lakes, streams and underground aquifers. In addition, this water may contain chemicals such as pesticides or nitrates that are “leached” out of the soil layers containing plant roots. In the model, precipitation that falls on soil whose water content is approaching saturation or on soil which is frozen flows directly off the soil into rivers, lakes or other drainage basins. The flow of water off the soil also depends on the slope of the land and the land cover. This flow of water is referred to as “runoff”.

 

• ·      “Mass balance” check. The model also performs a “mass balance” check for water. With a mass balance check, a calculation is made to make sure that all the precipitation can be accounted for as output (runoff, drainage, ActTrans, and ActEvap) or storage (change in soil water content). This is one way that errors in data or in the model equations can be checked for.

 

• ·      Outputs of the model (for example soil water contents) are put into columns in the ‘Output’ worksheet of the Basic GAPS workbook. These can be viewed directly or selected outputs can be displayed in graphical form as charts by clicking on the appropriate button on the ‘User Interface’ worksheet.         

 

 

 

A complete description of these processes and the entire GAPS model is located at: http://www.geo.cornell.edu/eas/index.html, click on “faculty”, click on “Susan Riha” and follow the links to GAPS.

 

 

 

 

 

 

 

 

 

 




4       Summary of the GLOBE data required by Basic GAPS

 

GLOBE Protocol                  GLOBE Data                         Input Data for Basic GAPS

                                                                                                Worksheet/Data name

Atmosphere/Climate:                                                         ClimateInput:

1) Air Temp.                             Daily max and min temp.          Max and Min Temp, C 

2) Automated Air & Soil Temp  Daily max and min temp           Max and Min Temp, C

3) Digital Multi-Day Max/Min/     Daily max and min temp                       Max and Min Temp, C

4) Precipitation                         Daily rainfall                              Rain, mm

                                                Daily snow (rain equivalent)      Snow, mm       

_______________________________________________________

Soil:                                                                                        SoilInput:

1) Soil Characterization            Horizon number                                    Horizon

                                                Root estimate                           Rel. Root Density

                                                Depth to top of horizon            Thickness, m

                                                Depth to bottom of horizon       Thickness,m

                                                Slope of site                 Slope

                                                Horizon texture (field)*              Horizon texture

2) Soil Particle Size Distribution Horizon texture (lab, USDA)*    Horizon texture

 

* If available, use the horizon texture data determined in the laboratory, as this data is more accurate than the field data. If those data are not available, use the horizon texture determined in the field.

Phenology:                                                                            ClimateInput:

1) Green-up                             Budburst date                          Budbreak Date

                                                Date of max leaf size                Full Leaf Date 

2) Green-down                         Leaves start change color        Start Sen. Date

                                                Leaves fall off                          End Sen. Date

                                                Latitude                                   Latitude

3) Budburst*                             Budburst date                          Budbreak Date

 

* If the budburst data is not in the Green-up protocol.

 

Land cover:                                                                           ClimateInput:

1) Land cover/Biometry            Canopy cover                           Fractional Land Cover

                                                (under Tree Biometry)

                                                Total ground cover

                                                (under Grass Biometry)

                                                                       

 


5       Summary Instructions for Running Basic GAPS

 

The following is a summary of the instructions for running Basic GAPS. Please read the previous background and descriptions of Basic GAPS before proceeding. You should have climate, soils, phenology and land cover data ready either from your own GLOBE investigations, by downloading these data from the GLOBE website, or by using the sample input data included with Basic GAPS (SoilInput Example and ClimateInput Example worksheets). Downloading the climate data requires more steps than the soils, phenology, and land cover data. Follow the instructions in Chapter 7 (Basic GAPS Model Inputs) for downloading climate data.

           

Running Basic GAPS

 

1) Open the Basic GAPS workbook. A dialog box will appear indicating that the workbook contains macros. These macros are legitimate macros that contain the equations for the model simulations. You need to enable these macros for the model to run.

 

2) Insert the climate data you have downloaded in the proper location in the ‘ClimateInput’ worksheet. If this worksheet is not visible, it can be made visible (“active”) by clicking on the command button labeled ‘Climate Data’ on the ‘User Interface’ worksheet or by clicking on the worksheet tab labeled ‘ClimateInput’ at the base of the Excel screen.

 

3) Go to the ‘User Interface’ worksheet by clicking on the worksheet tab labeled ‘User Interface’ at the base of the Excel screen. The ‘User Interface’ worksheet should appear (Fig. 2).

 

4) Click on the “Soils Data” command button under the ‘Enter Inputs’ heading on the ‘User Interface’ worksheet and enter the soils data following the screen instructions. You will return to the ‘User Interface’ worksheet after clicking “Done” on the soils dialog box, entering data in the runoff dialog boxes, and “OK” on the dialog box that contain cautions for data checking.

 

5) Click on the “Phenology/Land cover Data” command button, also under the ‘Enter Inputs’ heading on the ‘User Interface’ worksheet, and enter the phenology and land cover data. Clicking on “Done” and, after checking your data, clicking on “OK” on the data checking dialog box caution will return you to the ‘User Interface’ worksheet.

 

6) Click on the “Run Model” command button on the ‘User Interface’ worksheet.

 

7) There are two options for viewing model output: Excel charts (graphs) or Excel worksheet (table). These can be selected by clicking on the appropriate command button under ‘View Results’ on the ‘User Interface’ worksheet. Output can be viewed as graphs by clicking on the “View Graphs” command button. There are two options for viewing graphs: dynamically or static. Dynamic graphs actually show the data being plotted day-by-day while the static graphs show the data after the plotting is complete. Output can also be viewed as a table in an Excel worksheet by clicking on the “View Table” command button. This Excel worksheet can also be viewed by clicking on the ‘Output’ worksheet tab at the bottom of the Excel workbook.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

6       Basic GAPS Excel Workbook: The ‘User Interface’ worksheet.

 

Basic GAPS is designed so that users access the model through worksheets in an Excel workbook called “Basic GAPS”. When the workbook is brought up, the main “user interface” menu to input data, run the model and view output from the model is displayed on the active worksheet. Additional worksheets for each of these tasks are labeled ‘User Interface’, ‘SoilInput’, ‘ClimateInput’, and ‘Output’ and appear on tabs at the bottom of the screen. Each worksheet can be made visible (“active”) by clicking on its tab. Prior to the main user interface menu appearing, there will be a dialog box indicating that the workbook contains macros. These macros are legitimate macros that contain the equations for the model simulations. You need to enable these macros for the model to run. The ‘User Interface’ worksheet is briefly described below. The remaining worksheets will be described in the following sections as we go through the inputs and output of the Basic GAPS model.

 

The “Basic GAPS” workbook also contains example worksheets labeled ‘SoilInput Example’, ‘ClimateInput Example’ and ‘Output Example’. The tabs with these worksheet names are also visible at the bottom of the workbook. As mentioned above, data from the ‘SoilInput Example’ and,‘ClimateInput Example’ worksheets can be copied and pasted into the ‘SoilInput’ and ‘ClimateInput’ worksheets if you would like to try out the model right away. Output from a model run using these data is shown in the ‘Output Example’ worksheet. This allows you to familiarize yourself with the operation of Basic GAPS before entering and downloading your own data.

 

‘User Interface’ Worksheet

 

The ‘User Interface’ worksheet is the start of the program. It is shown in Figure 2A. This is referred to as the “user interface” because all model operations are done from this worksheet. This worksheet has three sections.

 



 

         Figure 2. User Interface. This worksheet is the user interface for                              Basic GAPS and will be visible (active) when the Basic GAPS                                  workbook is opened. The ‘User Interface’ worksheet contains the                         dialog boxes for inputting soils, climate, phenology, and land                                              cover data, running the model, and viewing model output.

 

The first section (‘Enter Inputs’) has three command buttons: “Soils Data”, “Climate Data”, and “Phenology/Land cover Data”. When these command buttons are clicked, forms will appear for entering soils, climate or phenology/land cover data. These are explained in detail in Chapter 7 (Basic GAPS Model Inputs). Climate inputs are entered directly into the ‘ClimateInput’ worksheet that is activated when the “Climate Data” command button is clicked. Soils, phenology, and land cover data are entered via dialog boxes that appear when you click on the “Soils Data” and “Phenology/Land cover Data” command buttons. These dialog boxes will prompt you for the soils, phenology, and land cover data.

 

The second section (‘Run the Model’) has one command button, “Run”. This is clicked when all the input data has been entered and the model is ready to start the simulations.

 

The third section (‘View Results’) has two command buttons, “View Graphs” and “View Table”. These allow the user to view the data as a graph or as table. The Basic GAPS inputs and output are described in more detail in Chapters 7 (inputs) and 9 (output).

                       

 

           

7       Basic GAPS Model Inputs

 

Considering Data Quality and Accuracy of Results

 

One of the goals of the GLOBE program is to educate students about the linkages between different parts of the natural system: soils, plants, climate, hydrology, and the atmosphere. The user-friendly software of Basic GAPS is an excellent tool for examining natural systems and the linkages between them. It is critical to recognize, though, that the output of Basic GAPS is only as good as the input data. This is generally not a problem if you are collecting all the data you need for Basic GAPS at your GLOBE site and have followed the instructions provided by the GLOBE protocols. However, if you are downloading data from the GLOBE website to use in Basic GAPS, we suggest several guidelines to maintain the quality of your input data and, therefore, the quality of the model output:

 

·      Make sure that the soils, climate, phenology, and land cover data are collected from the same general location (latitude, elevation, physiographic region/land classification). Why? Because, as mentioned above, there are linkages between the components of the natural system. For example, if you are interested in modeling a particular location near your GLOBE site you should try to get all input data for Basic GAPS from that area. You do not want to use soils data from a site that is very different from the site where the phenology, land cover, and/or climate data was collected from because soil has a significant impact on plants and this impact varies in a complex way with climate.

 

·      We also recommend that you check the “Site Info” section under the Search Results for the GLOBE site data that you want to download. Look at the soils, climate, phenology, and land cover site descriptions and check whether they are at similar geographic areas and elevations. If it wasn’t, the soil data may not represent the area where the climate, phenology, and land cover data were collected. This could lead to model outputs that do not represent (within the limits of the Basic GAPS model) the system you are interested in modeling (e.g. a local forest). Please contact us if you have any questions. Check for anything unusual that may affect the quality of the input data.

 

·