WQMAP User Manual Version 5.

January 2004
Headquarters: Narragansett, RI Phone: 401-789-6224 Fax: 401-789-1932 asa@appsci.com www.appsci.com Worldwide Offices: Castetbon, France St. Andrews, Scotland So Paulo, Brazil Gold Coast, Australia Perth, Australia

APPLIED SCIENCE ASSOCIATES, INC.

Table of Contents

About WQMAP .................................................................. i

Grid Generation ........................................................................................................... i Hydrodynamic Model.................................................................................................... i Pollutant Transport Model............................................................................................. i WASP Eutorophication Model ........................................................................................ i

1. Getting started ........................................................... 1

Technical Support ....................................................................................................... 1 Installing WQMAP for Windows .................................................................................... 1

2. Model Scenario Outline................................................ 2

Hydrodynamic Model................................................................................................... 2 Mass Transport Model ................................................................................................. 2

3. File Menu ................................................................... 3

The Scenario .............................................................................................................. 3 Geographic Locations and Base Maps ........................................................................... 4 Creating new Base Maps......................................................................................... 4 Selecting a Base Map ............................................................................................. 5 Non-Raster WQMAP........................................................................................... 5 New Location ............................................................................................................. 6 Creating a New Location from the WQMAP CD-ROM.................................................. 6 Creating a New Location from an External File.......................................................... 7 Display Settings.......................................................................................................... 8 Measuring Distances & Areas ....................................................................................... 9 Exporting Images ....................................................................................................... 9

4. Zoom Menu .............................................................. 10

Create Zoom Window................................................................................................ 10 Zoom In Previous ..................................................................................................... 10 Zoom Out Previous ................................................................................................... 11 UnZoom All .............................................................................................................. 11 Pan Map .................................................................................................................. 11 Saving Zoom Windows .............................................................................................. 11 Zoom to layer........................................................................................................... 12

5. GIS MENU ................................................................ 13

Understanding GIS objects and Layers ....................................................................... 13 The Active Layer....................................................................................................... 13 Displaying GIS Layers ............................................................................................... 14 Editing GIS Layer Characteristics................................................................................ 14 Adding GIS Objects................................................................................................... 15 Interrogating GIS Objects.......................................................................................... 17 Link Files ................................................................................................................. 18 Editing the Attribute Data of GIS Objects .................................................................... 19 Moving and Copying GIS Objects ............................................................................... 22 Moving Polyline and Polygon Vertices ......................................................................... 23

Deleting GIS Objects................................................................................................. 24 Renaming, Adding, and Deleting GIS Layers ............................................................... 25 Change Layer Position in GIS Layer List ...................................................................... 28 Field Type ................................................................................................................ 28 Editing the Attribute Table Structure .......................................................................... 29 Editing GIS Object Drawing Features.......................................................................... 30 Select Sets ............................................................................................................... 31 Color Coding GIS Objects in a Layer ........................................................................... 34 GIS Databases.......................................................................................................... 34 Adding GIS Databases .......................................................................................... 34 Changing GIS Databases ...................................................................................... 35 Attaching External Files to GIS Layers ........................................................................ 35 ArcView/ArcInfo Shape files .................................................................................. 36 Microsoft Access and dBase Tables ........................................................................ 36 Attaching an Access or dBase Table....................................................................... 36 ASA GDW Files .................................................................................................... 37 ArcView FLT Grid Files .......................................................................................... 37

6. Data menu ............................................................... 38

Edit Grid Cells........................................................................................................... 38 Select Grid Cells by Region ........................................................................................ 38 Add Time Series Site ................................................................................................. 38 Add Load Site........................................................................................................... 38 Winds ...................................................................................................................... 38 The Wind Data Editor ........................................................................................... 38 Entering Wind Data .............................................................................................. 39 Editing Wind Data ................................................................................................ 41 Importing Wind Data............................................................................................ 42 View Bathymetry Database........................................................................................ 43 View Open Boundary Database .................................................................................. 43

7. Run Model Menu....................................................... 45

Run Hydrodynamic Model.......................................................................................... 45 Run Control ......................................................................................................... 45 Model Parameters ................................................................................................ 45 Physical Parameters ............................................................................................. 46 Run Mass Transport Model ........................................................................................ 47 Run Batch Mode ....................................................................................................... 48 Running a New Simulation......................................................................................... 48 Viewing Trajectory Model Results ............................................................................... 48

8. Model Output ........................................................... 49

View Time Series Data .............................................................................................. 49 Section View ............................................................................................................ 49 Environmental Windows ............................................................................................ 49 Export Time Series Data............................................................................................ 49 Export Multiple Time Steps to Shape File .................................................................... 49

9. Tools Menu .............................................................. 50

Deleting Scenario Files .............................................................................................. 50 Importing/Exporting GIS Files .................................................................................... 50

TIE Files.............................................................................................................. 51 MIF/MID Files ...................................................................................................... 52 ESRI ArcView/ArcInfo Shape Files.......................................................................... 52 MOS Files ............................................................................................................ 53 Converting 16-bit layers to 32-bit layers................................................................. 53 Color Keys/Legends .................................................................................................. 53 Add Labels ............................................................................................................... 54 Export Grid to Mif/Mid file.......................................................................................... 54

10. Tides & Currents ..................................................... 55

View Tide Station Information.................................................................................... 55 View Current Station Information ............................................................................... 55

11. Help....................................................................... 56 12. Frequently Asked Questions ..................................... 57

Appendix .............................................................. 59
Appendix A: Directory Structure, Input and Output Files ............................................ A-1 Directory Structure.............................................................................................. A-1 HYDRO Input Files .............................................................................................. A-2 HYDRO Output Files ............................................................................................ A-3 MASS Input Files................................................................................................. A-4 MASS Output Files .............................................................................................. A-5 GRID Input Files ................................................................................................. A-6 GRID Output Files ............................................................................................... A-6 WQMAP Executables ........................................................................................... A-6 Appendix B: ASCII File Formats ............................................................................... B-1 Wind File Format - *.ASW.................................................................................... B-1 A Single Load Constituent File - *.ASL................................................................... B-2 Depth Import File Format - *.DPT ........................................................................ B-3 Atmospheric File Format - *.WNV ......................................................................... B-4 Open Boundary Tidal Forcing File - *.HST ............................................................. B-5 River Boundary Discharge File - *.RVR.................................................................. B-6 Appendix C. TIE Format for GIS Data Import/Export................................................... C-1 Appendix D. How to create base maps, process large polygon layers and work with GIS layers and SHP files .................................................................................................D-1 Managing GIS Data in SHP Files ...........................................................................D-1 SHP Files............................................................................................................D-1 Limits Imposed by the Operating System ..............................................................D-1 GIS Layers .........................................................................................................D-1 Attaching SHP Files as GIS Layers....................................................................D-2 Importing SHP Files into GIS Layers.................................................................D-2 Base Maps..........................................................................................................D-2 Attaching SHP Files as Base Maps ....................................................................D-2 Importing SHP Files into a Base Map................................................................D-2 Performing the Intersection of two Polygon Layers ................................................D-2 Appendix E: Helpful Websites to determine Environmental Data ................................. E-1 Metrological Data ................................................................................................ E-1 Bathymetric Data ................................................................................................ E-1

About WQMAP
WQMAP is a hydrodynamic and water quality modeling system developed for use in marine and fresh water environments. The WQMAP modeling system is composed of several integrated components. Model components include two or three dimensional, time dependent numerical solutions to the basic conservation equations for water mass, momentum, constituent mass, energy, salt, sediment, etc. These models simulate a wide range of physical, chemical, and biological processes in various types of water bodies. They can help to elucidate system dynamics and to predict the impacts of actual events or possible alternatives. The models can be used to estimate currents and water surface elevations, assess water quality and eutrophication problems, identify pollutant sources, and perform environmental impact assessments. WQMAP also includes an embedded Geographic Information System (GIS). The GIS is used to store, display and analyze any type of geographically referenced data. Types of data often included in the GIS are place names, critical habitats for fish and wildlife and environmental data. These data are not necessarily used by the models, but they are often helpful in analyzing and interpreting model results. The version of WQMAP you are using will contain one or more of the following model options: Grid Generation The boundary conforming grid generation software, is a tool to build a grid, which tiles the water body of interest into discrete volumes that are input to the models. The user species essential grid nodes (grid corners) along the domain boundary. The model then interpolates the remaining boundary node locations and solves a Poisson equation to locate the interior nodes. Editing tools to add and delete nodes as well as moving nodes are included. The resulting nonorthogonal boundary conforming grid contains quadrilaterals of various sizes and orientation to both resolve fine detail where needed and cover large areas. The hydrodynamic and water quality models then use this grid to numerically solve the appropriate conservation equations. Hydrodynamic Model The hydrodynamic model solves the water mass and momentum equations on curvilinear grid to predict a time varying field of surface elevations and velocity vectors. Environmental forcing includes tides, winds, river flows and density distributions. The basic model is configured to run in a vertically averaged mode. As an option, a full three-dimensional, coupled prognostic, baroclinic version of the model can be incorporated. Pollutant Transport Model The single constituent pollutant transport model solves the conservation of mass equation which includes a first order loss rate term and settling. Single and multiple, constant and time varying loads can be applied. The basic model is configured to run in a vertically averaged mode. As an option, a full three-dimensional constituent transport model can be incorporated. Constituents can include pathogens, excess temperature, metals, nutrients, organics and conservative tracers. WASP Eutorophication Model For the eutrophication model, the pollutant transport model has been enhanced to model eight state variables using the Eutro WASP kinetic rate equations. The vertically averaged version is configured with one water column layer and a sediment layer. The BFWASP model may be optionally configured in a fully three-dimensional mode.

1. Getting started
Thank you for choosing WQMAP for Windows. This manual repeats and expands on the on-line help also available to the WQMAP User. It is strongly recommended that the user works through the WQMAP manual to achieve maximum understanding of WQMAPs functionality. This user manual describes each WQMAP command in the order in which they appear in the pull-down menus.

Technical Support
Technical support is available for WQMAP users from 9:00 a.m. to 5:00 p.m. eastern time, Monday through Friday; phone (800) 780-6224 or fax (401) 789-1932. WQMAP support questions may also be sent via e-mail to: asa@appsci.com.

Installing WQMAP for Windows

To install the WQMAP system the software requires a VGA color monitor, a Microsoft-compatible mouse and an IBM-compatible 486 or better PC; with 64MB RAM, 100 MB free disk space on the hard drive running Microsoft Windows 95 or newer. Install WQMAP: 1. Insert the installation CD. 2. Using Windows Explorer, run the SETUP.EXE from the CD. 3. Follow the instructions on the screen. 4. When installation is complete, you will have a new program group labeled WQMAP, with an icon for the WQMAP model system.

-1-

2. Model Scenario Outline

In the following pages is an outline of how to run of WQMAP using the hydrodynamic model. The following chapter is intended to introduce you to the system and the components you will need in setting up and running typical scenarios. A more detailed description of how to run a simulation is explained in the Getting Started Manual.

Hydrodynamic Model
1. From the File menu, select New Scenario. 2. Select Hydrodynamic Model, enter scenario name and select if the model is to be run as a 2-D or 3-D case. If a 3-D simulation is selected, the number of layers in the z directions has to be entered. If available select the appropriate grid and time-series data. 3. From the Run Model menu, select Hydrodynamic Model. Fill in all the appropriate values on the Run Control, Model Parameters, and Physical Parameters tabs. 4. Once the necessary input data has been specified and the scenario has been defined, the model can be run, select Hydrodynamic Model. For information on entering input data see the Run Model Menu, Run Hydrodynamic Model. 5. While the model runs, a status window will show the progress of the simulation. 6. After the model is complete, view model animation.

Mass Transport Model

1. From the File menu, select New Scenario. 2. Select Mass Transport Model, enter scenario name and hydrodynamic file to use. If available select the appropriate grid and time-series data. 3. From the Run Model menu, select Run Mass Transport Model. Fill in all the appropriate values on the Run Control form. 4. Once the necessary input data has been specified and the scenario has been defined, the model can be run, select Hydrodynamic Model. For information on entering input data see the Run Model Menu, Run Hydrodynamic Model. 5. While the model runs, a status window will show the progress of the simulation. 6. After the model is complete, view model animation.

-2-

3. File Menu
Scenarios are the means of organizing model data and parameters into unique collections. A scenario in WQMAP is a collection of information that defines a model simulation. This information includes a definition of the environmental data files used in the simulation, saved under a unique scenario name. There are several options available under the File menu for handling scenarios, which shall be discussed in the following section.

The Scenario
Before a model simulation is run, a scenario is only the set of input forms defining the input data. After the execution of a model simulation, a scenario also has model output associated with it, which may be displayed. Thus the term scenario is used to describe both the inputs and the outputs of a model simulation. In WQMAP there is always one active scenario. The active scenario name is displayed at the top of the screen, and the components of the scenario can be viewed in the map window or a more explicit description is under the Model Output Scenario Information.

New Scenario is used to specify a new scenario. For this option select the type of model to be run, specify the scenario name, and select appropriate input data. The following form appears:

-or Open Scenario is used to open a previously defined scenario and the results of the simulation. The scenario selected becomes the active scenario. Its name is at the top of the screen and the simulation output can be displayed in the map window. An explicit description of the scenario is under the Model Output Scenario Information. The following forms appears:

-3-

Save Scenario is used to save any changes made to the data of the active scenario. Save Scenario As is used to save the active scenario under a different name. Edit Scenario is used to change the time-series data (and mass loads for a mass transport scenario) associated with the active scenario. Changes made using Edit Scenario are automatically saved.

Geographic Locations and Base Maps

Each WQMAP application is specific to a particular geographic location. All data, scenarios and model output are stored within this location. The location consists of an area defined by its outermost longitude/latitude coordinates. The location is given a name and contains a base map depicting land and water. The name of the active location is displayed at the top of the map screen. WQMAP can have any number of locations. To move between locations, select Geographic Location from the File menu. The available locations will be listed under the \WQMAP\LOC_DATA\ directory. Click on the desired location to make it active, and then click on OK. Read more about creating new locations. A geographic location can have multiple base maps. The base map displayed for the active geographic location can be changed by selecting Base Map from the File menu, then selecting the desired file for the new base map. Base maps can be either a vector map drawn from a set of longitude, latitude coordinates, or a raster image which has been registered to longitude, latitude coordinates.

Creating new Base Maps

The base map in WQMAP displays the land and water features for the active geographic location. Base maps can be created from MapInfo (mif/mid) files or ESRI ArcView (.shp) files Each geographic location can have multiple base maps, but only one base map is displayed at any time. The base map files can be stored on a local hard disk or network disk drive, or on CDROM.

-4-

Vector base maps consist of polygons depicting the land features within an area. When drawn in the map window, the land polygons are drawn in one color (e.g. green) on a background of a different color (e.g. blue). To create a new vector base map file, generate land polylines or polygons using geographic coordinates in one of the base map formats. Raster base maps are bitmaps created by scanning a paper map into digital form. A raster base map captures all the features on the paper map and creates a fixed image of the map. Two raster base map formats (BSB Electronic Charts, and Resolution Mapping/Maptech) are commercially available on diskette for single charts or on CD-ROM for all charts within an entire region. These charts are available at most nautical supply stores.

Selecting a Base Map

Change the base map displayed in the current geographic location by choosing Base Map from the File menu. In the Map Files dialog, select a file type by clicking the button next to one of the available types. Next, select the disk drive and directory where the file exists, and then highlight the file to be used. Click OK. The selected base map will be active in the current geographic location until a different file is selected.

Non-Raster WQMAP

Raster WQMAP

-5-

New Location
To create a new geographic location in WQMAP you must first create a new base map. There are two options for creating a new geographic location: Import data from a WQMAP CD-ROM containing digital coastline data. Import a new vector or raster base map. Both of these options are available under the File-> New Location menu.

Creating a New Location from the WQMAP CD-ROM

WQMAP may be supplied with CD-ROM databases. These databases generally contain vectorbased coastline data from a variety of sources (i.e., Digital Chart of the World, World Vector Shoreline, Digital NOS charts). They may contain additional data such as place names, wind stations, depth data, and/or other environmental or geographic information. The CD-ROM may be used to make a new location for WQMAP. To do so, place the CD in the CD-ROM drive. From the File menu, select New Location and then select World Database. A form will appear on which to specify the name for the new location, the geographic extent of the new location, and the type of data to be used to create the new shoreline.

-6-

Enter a name for the new location, and select the source data type. Zoom in or pan to the desired region on the world map in the World Database window, then click on Create Location. A new location will be created from the database. The new location will automatically create a large grid for the region.

Creating a New Location from an External File

Creating a new location from an external file involves selecting a base map file of one of the available base map file types. (See the discussion under Geographic Locations and Base Maps)

-7-

From the File menu, select New Location and then select Import Map File. The Location Import window will open, enter a name for the new location and then click on Browse to select the base map file to import. In the Map Files dialog, select a file type and select the disk drive and directory where the file exists, and then highlight the file to be used. Click OK. You will be returned to the Location Import dialog where you click Create Location. The selected base map will be used in the new geographic location.

Display Settings
Several options are available to adjust the WQMAP map display. These options include the colors and measurement units used, and the map projection. Most of the map settings that can be changed are accessed through the Display Settings option of the File menu. Optionally, right-click on the map window and select Map Display Settings. This option brings up a form to: Select the colors used for land, water, land outline, current vectors, and the longitude/latitude grid. To select colors, click on the color box to bring up a color menu. Specify whether the land outline and the longitude/latitude grid are shown on the map. Check the box to the right of these fields to display them. The current vector display options allows the use the standard line vector or thicker area vectors. Specify the units used for longitude and latitude. Toggle the field between decimal degrees (DD.DD), degrees and decimal minutes (DD MM.MM), and degrees-minutesseconds (DD MM SS). Specify the units used for current vectors. Toggle the field between mm/s, cm/s, m/s, and knots. Specify whether a distance scale is displayed on the map. Check the box to display the distance scale. Read more about . Specify whether or not to use a 24 hour clock to report times.

-8-

Measuring Distances & Areas

To get the distance between two points, select the Distance Measure icon on the toolbar. Click on the point from which to measure distance. This sets one end of the measurement line. As you move the cursor around, the distance between the set point and the cursors position is given at the lower left of the map. Clicking again with the left button will start another measurement line segment. The total cumulative distance of all the line segments is displayed on the status bar. Double-click with the left mouse button to close the polygon and get the area of the polygon. Press the Esc key to exit the distance measurement mode.

Exporting Images
Under the File menu, an export utility is included for creating graphics of the active scenario.

-9-

4. Zoom Menu
There are several options available under the Zoom menu for handling scenarios, which shall be discussed in the following section. Several Zoom options are available to change the scale of the map display. Using these options the scale of the map can be increased or decreased, and the center of the map display can be shifted. All these options are available under the Zoom menu.

Create Zoom Window

To zoom in on an area of the map display: 1. Select Create Zoom Window from the Zoom menu - OR - click on the Create Zoom Window icon 2. 3. 4. on the WQMAP toolbar.

Move the zoom pointer to one corner of the area to zoom into. Hold down the mouse button and drag a box around the area to zoom into. Release the mouse button, and the new zoom window will be created.

To zoom out around an area of the map display: 1. Click on the Zoom Out icon on the WQMAP toolbar.

2. Position the zoom pointer over the area to zoom out, and click. A larger view of the map will be displayed; the location where the mouse was clicked will be in the center of the map window.

Zoom In Previous
To return to a previous zoom window at a larger scale:

- 10 -

1. Select Zoom In Previous from the Zoom menu. 2. Each time you select Zoom In Previous, the zoom window previously created at a larger scale than the current window will be displayed.

Zoom Out Previous

To return to a previous zoom window at a smaller scale: 1. Select Zoom Out Previous from the Zoom menu. 2. Each time you select Zoom Out Previous, the zoom window created at a smaller scale than the current window will be displayed.

UnZoom All
To return to the original map scale: 1. Select Unzoom All from the Zoom menu.

Pan Map
To re-orient the zoom window: 1. Select Pan Map from the Zoom menu or click on the Pan Map icon. 2. Position the hand cursor on the map and drag the hand to move the map display on the screen. For example, if an island appears at the lower left of the map display and you want to re-orient the display so the island is in the center, position the hand on the island, drag it to the center of the display, and then release. The window will be redrawn at the same scale with the island in the center.

Saving Zoom Windows

It is possible to save the current set of zoom window views. This might be useful, for example, when you wish to print standard views of a location while still being able to zoom in and out of other parts of that location.

- 11 -

To save a set of views: 1. 2. Select Save Current Zoom Windows from the Zoom menu Give the file an appropriate name (it will take a ZSV extension), and click on Save.

To recover a set of views 1. 2. Select Open Previous Zoom Windows from the Zoom menu Select the desired file and click on Open.

This utility saves both the zoom views as well as the map window size and shape that was current when saved.

Zoom to layer
By right clicking on the active layers window, the user may zoom to the location of that particular layer.

- 12 -

5. GIS MENU
Understanding GIS objects and Layers
WQMAP contains an embedded Geographic Information System (GIS). The GIS is a system for storing, retrieving, and displaying geographically referenced data. The primary use of the GIS is to complement the display of model predictions by showing the models results in relation to sites and items of interest. Any type of data with a specific geographic location can be stored as a GIS object. A GIS object can be one of four distinct types: A point is an object with a single location. A line is an object stored with two locations defining its end points. A polyline is a line with more than two points. A polygon is a closed polyline. It may be filled with different color/pattern combinations and is used to represent map features having area. Polygons, rectangles or squares can be created. Note: Circle polygons cannot be exported to a shape file.

Each object in the GIS database, as well as having a geographic position, may also have text, number, and/or picture information attached to it. This is called attribute data and is stored in Microsoft Access database tables. GIS objects are grouped in layers, and any number of layers are then grouped into a GIS database. The layers available for the current GIS database are listed in the GIS Layers window. Layers typically contain objects with similar characteristics, such as a layer of place names, or a layer of shellfish beds. A layer can contain all four types of objects. Any number of layers can be contained in a single GIS database. Additional GIS databases may be created to organize data, but only layers from a single geographic database may be displayed on the map at one time.

The Active Layer

Only one layer of the GIS can be active at a time. The active layer is the layer to which all data are added when new objects are entered into the GIS. The active layer also controls the availability of different editing functions such as Move. The active layer is designated with a raised look in the GIS Layers window. To change the active layer click on the layer which is to become the active layer. The new active layer will then be raised in the GIS Layers window.

- 13 -

Cities is the Active layer.

A listing of all objects in the active layer can be obtained by selecting Active Layer Table from the GIS menu. This displays an Access table showing each object and its stored attributes.

Displaying GIS Layers

Not all layers in the GIS database need to be displayed at once. The GIS Layers window controls which layers are displayed on the map and which layer is the active layer. This window is always open. Use the window to toggle on/off the GIS layers to be shown on the map, and to set the active layer. When you have checked the layers that you wish to be displayed, click the Redraw button on this form to redraw the map with the selected layers on/off OR you may double click on the on/off check boxes and the map will automatically redraw. The Labels button on this window allows the user to toggle all the layer object labels on or off. You may set specific layers to display labels by using the Layer Tools form see Editing GIS Layer Characteristics. Read more about Renaming, Adding and Deleting GIS Layers.

Editing GIS Layer Characteristics

To set the display characteristics of objects by layer, select Layer Tools from the GIS menu, or double click on the name of the layer that you wish to edit. This brings up a form on which to specify: the layer whose characteristics are to be set, the icon style and size used to represent point objects. Click on the icon box to bring up the font/size menu. the line color, style and width used to represent line and polyline objects. Click on the line box to bring up the color menu.

- 14 -

the color, pattern and style used to represent polygon objects. Click on the polygon box to bring up the color/pattern menu. whether or not labels are to be displayed with point objects, the layer attribute to use as a label, and the font characteristics of the labels.

This form is also used to Add, Delete and Attach layers to the active GIS database.

Adding GIS Objects

Objects are added to GIS layers using the mouse to set the position of the objects. All objects are added to the active layer. To add objects to the GIS: 1. 2. 3. In the GIS Layers window set the active layer by clicking on the desired layer. Check that the active layer is raised. Otherwise the objects entered will not be visible until the layer is turned on. Select Add Object from the GIS menu, then select the object type from the Add Object drop-down menu - OR - click on the appropriate icon on the toolbar.

- 15 -

4.

To add: Points - Click the mouse cross-hair at the location for the point. The longitude/latitude position of the cross-hair is displayed at the bottom right of the screen. Lines - Click the mouse cross-hair at the location for the first point in the line, then move the cross-hair to position the end point of the line and click to place the end point. The longitude/latitude position of the cross-hair is displayed at the bottom right of the screen. PolyLines - Click the mouse cross-hair at the location for the first point. The longitude/latitude position of the cross-hair is displayed at the bottom right of the screen. Then move the cross-hair to position the next point in the polyline and click. Repeat this for all vertices in the polyline. Double-click the left mouse button to end the polyline. The point set by this final click is not part of the polyline. Polygons - Click the mouse cross-hair at the location for the first point. The longitude/latitude position of the cross-hair is displayed at the bottom right of the screen. Then move the cross-hair to position the next point in the polygon and click the mouse button. Repeat this for all vertices in the polygon. Double-click the left mouse button to close the polygon. The point set by this final click is not part of the polygon. Note: This will create a polygon to create a rectangle or circle you will need to go to the GIS menu select Add Object then Polygon Object.

5.

An attribute form will appear with the layer name in the header. Enter any desired information on the attribute form. If a link file field is available, attach text or graphic files to the object by clicking on the Link button at the bottom of the attribute form.

- 16 -

Click OK to add the object to the GIS database active layer.

Interrogating GIS Objects

Any object shown on the map can be interrogated to display its attributes. In the GIS Layers window check that the layer containing the objects to be interrogated is checked on. Objects do not need to be in the active layer in order to be interrogated. If the mouse cursor is not an arrow (indicating interrogate mode), select the interrogate mode by clicking on the interrogate icon on the toolbar.

Click on the object(s) to be interrogated. The Object Attributes window will appear, containing an Attributes tab, a Geo(graphical) Data tab, and a Drawing tab.

The Attributes tab lists the attribute data associated with the object and any link files. To list the attribute data in Notepad format, click on the List button at the top of the window. To view any link files associated with the interrogated object, double click on the field labeled LinkFile. The Geo tab provides the longitude and latitude position of point objects or the length or area of line or polygon objects.

- 17 -

The Drawing tab allows the objects appearance on the screen to be edited.

If interrogating multiple objects that occupy the same geographic location, the Next and Prev buttons of the Object Attributes window are used to move between them.

Read More About GIS Objects.

Link Files
Link Files are external files such as text files or picture files that are attached to a map object. Multiple link files may be attached to each map object. When the map object is interrogated, the Link File(s) attached to the object may also be viewed.

- 18 -

Microsoft Access tables attached to GIS layers are used to store the names of the link files. The names of link files are stored in a standard text field in the Access table. The WQMAP GIS recognizes the first four letters of the text field (e.g., Linkfile) and classifies the field as a Link File field. Any text field whose name begins with the letters LINK (e.g., Linkfile, Link field, Linked Object, Linked Response Plan) will be classified as a Link File field. If multiple link files are attached to one field, all of the names of these link files are stored in the text field. The length of this text field is set to the maximum (255 characters) so that as many link files as possible may be attached. If you add Link File fields to the Access table, you should ensure that these text fields are also set to 255 characters. To attach a link file to a map object, see To view attached link files, double click on the object in the map window or on the link file field with the camera icon in the Object Attributes window. If there is more than one link file attached, select which link file to view. WQMAP recognizes TXT, BMP, PCX, and AVI files automatically. Other file extensions will be viewed based on how they are associated in File Manager. You may associate file extensions with applications in File Manager or Windows Explorer, and WQMAP will use these relationships to view link files (i.e., if DOC files are associated with Microsoft Word, then WQMAP will open Microsoft Word to view a DOC link file).

Editing the Attribute Data of GIS Objects

The attributes of any object shown on the map can be edited. In the GIS Layers window check that the layer containing the objects to be edited is checked on. The objects do not need to be in the active layer. If the mouse cursor is not an arrow (indicating interrogate mode), select the interrogate mode by clicking on the interrogate icon on the toolbar.

Click on the object to be edited. To edit any of the attribute data, click on the Edit button at the top of the window. This will bring up the editing window containing all the attribute data. New data can be entered in any of the fields.

- 19 -

If link file fields are available, link files can be added or deleted. Click on the Link button to the right of the Link File field in the editing window. Alternately, double click on the Link File field in the Object Attributes window where the Open File icon appears. This will bring up a window showing the files currently linked with the object and allowing two options: Add Link File and Remove Link File. To remove a link file, first highlight the file to be removed and then click the Remove Link File button.

To produce a text file of the attributes contained for the GIS data click on List button at the top of the window. This will open WordPad with a text file containing all the attribute data.

To set a point objects position to a specific longitude and latitude, open the Geo Data tab and enter the desired longitude and latitude coordinates for the point. Click on the Apply button to save the object at the new position. Alternatively, select Move by Mouse, and move the mouse cursor/box that appears to the new location and click. The object will appear at the new location when the screen is redrawn, therefore do not click on Apply.

- 20 -

To change the objects appearance on the screen open the Drawing tab and click on the symbol.

An icon selector window opens were you may change the size, color and icon to be displayed on the map. After the icon has been selected click OK. You may either apply this symbol to that one object or all objects of this type.

- 21 -

Moving and Copying GIS Objects

Only objects on the active layer may be moved. Any type of GIS object can be moved from one location to another. Lines, polylines, and polygons are moved with all their vertices stationary (i.e, their shape and orientation is unchanged). To move an object: 1. 2. Use the GIS Layers window to make the layer in which the object is stored the active layer. Select Move Object from the GIS menu OR click on the Move Object icon on the toolbar.

- 22 -

3.

Position the mouse cross-hair over the object and drag the object to its new location while holding down the left mouse button. Release the mouse button to leave the object in the new location. To Copy an object, hold down the shift key while moving the object with the mouse.

4.

You may also move point objects by interrogating them and selecting the Geo tab in the Object Attributes window. The Geo tab provides the longitude and latitude position of point objects and provides a Move by Mouse option for all object types. To set a point objects position to a specific longitude and latitude, open the Geo tab and enter the desired longitude and latitude coordinates for the point. Click on the Apply button to save the object at the new position. For any object type, select Move by Mouse and the object will automatically be selected on the map and the cursor may be used to move the object to a new location. The object will automatically be moved, therefore there is no need to click on Apply.

Moving Polyline and Polygon Vertices

The vertices of polyline and polygon objects can be moved individually to reshape an object. To move the vertices of a polyline or polygon: 1. 2. Use the GIS Layers window to make the layer in which the object is stored the active layer. Select Edit Poly Vertices from the GIS menu, or click on the Edit Poly Vertices icon on the toolbar.

- 23 -

3. 4.

Position the mouse cross-hair over the polyline or polygon object. Click to select the object. The vertices will be highlighted. Position the mouse cross-hair over the vertex to be moved and drag the vertex to its new location while holding down the mouse button. Release the mouse button to leave the vertex in the new location. Repeat step 4 to move all desired vertices on the object. Double-click the left mouse button to stop moving vertices. You will be asked whether you want to save your changes.

5. 6.

Deleting GIS Objects

To delete an object from the GIS database: 1. 2. 3. Use the GIS Layers window to turn on the display of the layer the object is in. The layer does not have to be the active layer. In Interrogate mode, click on the object to be deleted. This brings up the Object Attributes window. Click on the Del button at the top of the Object Attributes window to delete the object. You will be asked to verify that you want to delete the object.

- 24 -

Renaming, Adding, and Deleting GIS Layers

Layers can be added and deleted from the active GIS database. The names of existing layers can also be changed. These capabilities are accessed through the Layer Tools option of the GIS menu, which brings up the Layer Tools window OR by right clicking on the active layer and selecting Layer Properties OR double click on the layer name in the GIS Layers window.

Right-click on active layer.

To change the name of a layer: 1. Select the layer to be renamed from the list of layers on the right side of the Layer Tools Window. It will be highlighted and its name will appear in the box at the top of the window. Enter the new name for the layer in the box at the top of the window.

2.

- 25 -

3.

Press ENTER or click on the OK button at the bottom of the window to save the new layer name.

To add a new layer to the database: 1. Click on the New Layer button at the bottom right of the window OR select Create New Layer from the GIS menu OR right click on active layer and select Add Layer. This will bring up a window in which to enter the name of the new layer. The default name is Layer n where n is the layer number.

Click on Add Field to define the data name and type of the first field and continue to add as many fields as required. Alternatively, select Defaults to use the WQMAP default data fields. The default structure of this table is shown below: Read more about Field Type. Field Name Name Description Text 1 Text 2 Text 3 Text 4 Text 5 Text 6 LinkFile

Field Type
Text[20] Text[20] Text[40] Text[40] Text[40] Text[40] Text[40] Text[40] Text[255]

- 26 -

3 4

Select OK to add the new layer to the end of the list of layers. The new layer will have the name you entered and will already be selected (highlighted). The position of the layer in the layer list can be changed. Read more about .

To remove a layer from the database: 1. 2. Select the layer to be deleted from the list of layers on the right side of the Layer Tools window. Click on the Remove Layer button at the bottom right of the window.

To add a layer from another database: 1. If the file name of the layer to be attached is not known, verify it by selecting that layer in the Layer Tools window and selecting Layer Info. The file name will be given under Geo File.

2. 3

Open the new database to which the layer will be added by selecting GIS Database in the GIS menu. Select Layer Tools in the GIS menu OR by right clicking on the active layer and selecting Layer Properties OR double click on the layer name in the GIS Layers window, and select Attach Layer. Select ASA GIS Layer on this window and find the appropriate file from the other database. When the selection is made, select OK and the new layer will appear on the list of layers.

- 27 -

Change Layer Position in GIS Layer List

The layer position in the GIS Layer List can be changed by accessing Layer Tools option of the GIS menu, which brings up the Layer Tools window OR by right clicking on the active layer and selecting Layer Properties OR double click on the layer name in the GIS Layers window. Use the arrows to the right of the GIS Layer list to move the layer up or down.

Move Layer Up

Move Layer Down

Field Type
Text Text or combinations of text and numbers, as well as numbers. Can contain up to 255 characters or the length set.

- 28 -

Integer Stores numbers from 32,768 to 32,767 (no fractions). Long Integer Stores numbers from 2,147,483,648 to 2,147,483,647 (no fractions). Single Stores numbers from 3.402823E38 to 1.401298E45 for negative values and from 1.401298E45 to 3.402823E38 for positive values. Double Stores numbers from 1.79769313486231E308 to 4.94065645841247E324 for negative values and from 1.79769313486231E308 to 4.94065645841247E324 for positive values. Date/Time Date and time values for the years 100 through 9999. Currency Currency values. Yes/No Displayed as true or false. A box that is checked for yes or not checked for no

Editing the Attribute Table Structure

Each GIS object has attribute information stored in a Microsoft Access table. This structure may be made up of text fields, number fields, boolean fields, memo fields, or date fields. The table may have as many or as few fields as desired. The only requirement is that the table contain one counter field that is indexed. The attribute table structure of existing layers may be edited by opening the appropriate MDB file using MS Access. To get the name of the MDB file for a layer: Select Layer Tools from the GIS menu OR by right clicking on the active layer and selecting Layer Properties OR double click on the layer name in the GIS Layers window. In the Layer Tools window, select the desired layer (if not already highlighted). Click on the Layer Info button to access the Layer Information window. The Database field in the Layer Information window gives the full path name of the MDB file for the layer.

- 29 -

For more information on Access Databases and Table structures, please consult the Microsoft Access documentation.

Editing GIS Object Drawing Features

Objects (points, lines, polygons) are all drawn by default with the drawing attributes of their layer. However, objects may also be interrogated individually and the drawing attributes changed individually. You may change the following drawing features: Point Objects Icon, icon size and label justification. Line/Polyline Objects Line style and line color. Polygon Objects Polygon style and polygon color. To do this click on the object that you wish to edit. When the Attributes window appears, select the Drawing tab to change the drawing settings.

- 30 -

To only change the object that is interrogated click Apply. If you select Apply to All Objects of this Type you will change any object of the same drawing definition on this layer to a new definition. For example, if you select an object with the boat icon on layer 1, you may change all objects that are the boat icon on layer 1 to a new object definition. Having set the drawing characteristics of individual objects, you may reset them to the layer drawing characteristics by using the Layer Tools option in the GIS menu section OR by right clicking on the active layer and selecting Layer Properties OR double click on the layer name in the GIS Layers window. Click the Reset All Objects to Layer Properties button to reset any individually changed objects on this layer back to the Layer Settings.

Select Sets
Select sets are groups of map objects you create so that certain operations can be performed on the entire group. Objects in a select set may be from different layers. Not all select set functions will work on objects in attached shape files. To interrogate several objects without selecting them individually, use the Select Set option of the GIS menu.

- 31 -

You may create a select set in a number of ways. Individually You may select objects individually by simply clicking on them while holding down the CTRL key.

By Rectangle You may select objects by drawing a rectangle on the screen and any objects inside that rectangle will be put into a select set. By Region You may select objects by drawing a polygon on the screen and any objects inside that polygon will be put into a select set. By Radius You may select objects by drawing a circle of particular radius on the screen and any objects inside that circle will be put into a select set. Read more about Color Coding Objects in a Layer. By Query You may create a Select Set by performing a database query on the underlying Access table for each layer. Any objects shown on the screen that satisfy the query will be put into the select set.

- 32 -

This example will select any objects in the Place Names layer with the word bay (not case sensitive) anywhere in the Name field. You may perform queries that check for numeric values or string values. Click on List Possible Values to see a list of unique values in the selected field. This will give a list of all the possible values in that field for the whole layer. The actual select set will include only those objects visible on the screen. If you use the Like operator for strings, you should note the following:

Like *bay will find any strings that end in bay. Like bay* will find any strings that begin in bay. Like *bay* will find any strings that contain bay.

A Select Set Listing table is displayed. Each layer represented in the select set is displayed in a separate table, selected from the drop-down menu. Clicking on Settings in this window will bring up the Select Set Drawing Features window in which the drawing features of all the objects included in the select set may be modified. Clicking on Apply in this drawing features window will then apply the selected drawing features to all of the objects in the current select set.

- 33 -

Color Coding GIS Objects in a Layer

The Select Set by Query function may be used to color code layer objects according to numeric or text values in any field. This works for polyline or polygon objects, and, as for other queries, only works for those objects within the present zoom view on the screen. To apply this function, open the layer query window, select the layer and field name to be encoded, and click on List Possible Values. Then click on Color Code by Unique Value. After a brief interval, each polyline or polygon object in the layer with a unique value in the selected field will be given a different color.

GIS Databases
Each geographic location in WQMAP can have multiple GIS databases to assist in organizing map data. Only one database can be active and displayed at any one time. Read more about Changing GIS Databases.

Adding GIS Databases

To create a new GIS Database, select New GIS Database from the GIS menu. In the GIS Database Name window, enter a name to identify the new database or use the default name. Click on OK to complete the creation of a new database.

- 34 -

The new database initially has only one layer, labeled Untitled, which contains no data (objects). Data can be added to this layer and new layers can be added. If there is current, habitat/depth or land-water files in the original database they will be transferred to the new GIS Database.

Changing GIS Databases

To switch to another database, select GIS Database from the GIS menu. From the list of available GIS databases select a new active GIS database.

Attaching External Files to GIS Layers

The WQMAP GIS can use certain external files as GIS layers. Attaching a file as a layer involves selecting the file and adding it to the layer list. ASA's native GIS format, ArcView shape files, access/dBase databases and ArcView FLT grids.

- 35 -

To attach a file, select Attach New Layer from the GIS menu. Select the file type that you wish to attach, and then select the file that you wish to attach. You may attach files that are stored on a network drive, or on another PC's hard disk if peer to peer networking is available. For best performance the files should be places in the GISDATA folder in the GIS folder of your location.

ArcView/ArcInfo Shape files

When Shape files are attached, no conversion or import is performed; WQMAP simply draws the shape file in its native format. Drawing attributes such as color and icon may be specified as for any other layer.

Microsoft Access and dBase Tables

WQMAP provides an easy way for point data stored in Microsoft Access (Version 2.0) or dBase IV tables to be displayed on a map. Any Access or dBase table containing numeric fields with longitude and latitude coordinates in decimal degrees can be attached as a GIS layer. For example, a table of marine petroleum terminals can be mapped if the table includes a longitude and latitude field. Once the database table is attached, any edits made in the table or new records added via Access will be updated in the WQMAP GIS each time WQMAP is started. In addition, any editing or new records added within the WQMAP GIS will update the Access or dBase table.

Attaching an Access or dBase Table

To attach a Microsoft Access or dBase table, select Attach New Layer in the GIS menu. Select Access/dBase Database from the layer attachment options.

- 36 -

Select the database that holds the table you want to attach. For Access the database file extension is .mdb, for dBase the tables are in files with a .dbf extension. In addition, you must specify the fields that store the longitude and latitude information.

Click on the Attach button to make the attachment and create the new layer. This layer is said to be "geolinked". Geolinked means that any changes made in this layer within WQMAP are automatically reflected in the Access or dBase table. In addition, if GIS objects are added to this layer, records will also be added to the table that contains the objects.

ASA GDW Files

Attaching GDW files is most commonly used to re-attach a layer that was previously removed from the layer list. This brings the layer back into the layer list. You may attach files that are stored under another location so that different locations may share common layers, or files that are on a network drive, or on another PC's hard disk if peer to peer networking is available.

ArcView FLT Grid Files

Gridded data created in ArcView Spatial Analyst may be attached in order to overlay spatially interpreted data such as habitat maps or shoreline types on the base map of the model location.

- 37 -

6. Data menu
The data menu allows the user to edit and display certain hydrodynamic and mass transport model input conditions. For more detailed application information refer to the WQMAP Getting Started Manual.

Edit Grid Cells

This option allows the user to paint in initial conditions for salinity and temperature as well as define spatially variable bottom friction coefficients to individual cells. As well as set river and open boundary conditions.

Select Grid Cells by Region

This option allows the user to paint in initial conditions for salinity and temperature as well as define spatially variable bottom friction coefficients to groupings of cells. As well as set river and open boundary conditions.

Add Time Series Site

This option allows the user to create a GIS point object that will store the model output from a specific location in a time series format. This model output can then be visualized within the user interface or exported for further analysis.

Add Load Site

This option is only available when working with a mass transport scenario. It allows the user to specify mass loading conditions (flow and concentration) using a GIS point object.

Winds
The wind data required for a model simulation consists of a series of wind speeds and directions covering the time period being modeled. WQMAP contains a Wind Data Editor to facilitate the task of entering wind data.

The Wind Data Editor

The Wind Data Editor contains tools to input and display wind data. A dart board is used to input wind speed and direction with a simple point and click technique. Alternately speed and direction can be manually entered. A time increment setting is available so that wind data do not need to be input at hourly intervals. To view the data in the wind file a listing of each wind speed and direction entered is provided, along with a stick plot showing. The dart board is the quickest way to enter wind data. The rings of the dart board correspond to different wind speeds (in knots), increasing in speed away from the center. The direction from which the wind is blowing is indicated by the clockwise angle (0 to 360 degrees) around the rings of the dart board. As you move the mouse around the dart board, the wind speed and direction corresponding to the mouses position are displayed in the text box above the dart board. Clicking the mouse on the dart board adds a wind record to the wind file. The wind data you enter is assumed to follow the meteorological convention: the direction is the direction FROM WHICH the wind is blowing. The stick plot which

- 38 -

displays the wind data follows the oceanographic convention: the direction is the direction TOWARD WHICH the wind is blowing. Note: The wind data editor can not display wind records larger than 43,500 time steps. This would be approximately 4 years of hourly data.

Entering Wind Data

The following steps describe the process of creating a new wind file. 1. Start the Wind Data Editor by selecting Enter/Edit Winds from the Data menu.

2.

Set the time Increment (in hours) at which data will be entered. At the lower right of the Wind Data Editor window is the Increment box with up/down arrows to increase/decrease the increment. The time increment is the duration that each wind speed/direction entry will last. For example, a 6 means that each wind observation is valid for the next six hours. At any point while entering wind data, the time increment can be changed. From the Wind Data Editor File menu select New File. Enter a name for the wind file and set the start date and time for the new file.

3.

- 39 -

Clicking in the box for the date/time entry brings up a calendar from which the date and time can be selected. To use the calendar click on the desired year, month and day of month on the calendar display. To select the current days date, click on the Today button located below the monthly calendar. Use the up/down arrows to the right of the hour and minute boxes at the bottom of the calendar to select the time the wind record is to begin. Click on OK to save the selected date/time and return to the New Wind File window.

The default coordinates for the wind station will be the center of the map. However, wind stations are represented in a GIS layer (Wind Stations) and may be moved like any GIS object. If multiple winds will be used, it is important to enter the correct coordinates for each station.

- 40 -

4.

A default wind speed box opens you can enter in a default value (in knots, m/s or force) and direction (meteorological or degrees) or to enter using the dart board click update.

Entering wind speed and direction records by clicking on the dart board. This will allow manual entry of wind values. Note if the ADD RECORD button is grayed out, to make it active ensures that you are at the end of the record. To use the dart board, place the mouse on the dart board at the desired wind speed and direction, and click. Each click of the mouse on the dart board generates one entry in the time series. The wind data entry is added to the table to the left of the dart board and to the stick plot graph at the lower left of the Wind Data Editor window. The Add Record manual entry window allows the use of alternate units of wind data entry. 3. 4. When all data have been entered, select Save File from the File menu to save the file. The table and the stick plot will clear. Exit the Wind Data Editor by selecting Exit from the File menu.

Read more about Editing Wind Data and Importing Wind Data. $$$

Editing Wind Data

The following steps describe the process of changing an existing wind file. Existing wind data entries in the file can be changed and new wind records can be added to the end of the file. 1. 2. Start the Wind Data Editor by selecting Enter/Edit Winds from the Data menu. Select Open File from the Wind Data Editors File menu. Select the name of the wind file to be edited. Click OK to continue.

- 41 -

3.

To change existing wind data entries: Scroll through the wind record listing to the date and time for which wind data will be changed. Click on the data entry to be changed (it will be highlighted). To use the dart board to change the wind speed and direction, place the mouse on the dart board at the desired wind speed and direction, and click. The speed and direction corresponding to the mouses position are shown in the text box above the dart board. To change data by typing the speed and direction, double click on the entry to be edited or highlight the entry and select Edit Record.

4.

To add more wind data to an existing wind record: Scroll to the end of the wind record listing. Add wind records by clicking on the dartboard or by using the Add Record button at the end of the data file.

5. 6.

When all changes have been made, select Save File from the File menu to save the file. The table and the stick plot will clear. Exit the Wind Data Editor by selecting Close from the File menu.

Importing Wind Data

A wind data file can be created in the ASW format (see Appendix) using a text editor and imported into WQMAP for use in the models. To import an ASW wind file: 1. 2. 3. From the Data menu select Enter/Edit Winds. Select Import ASW File from the File menu of the Wind Data Editor. Select the file to be imported.

- 42 -

View Bathymetry Database

This option allows the user to visualize the global gridded ETOPO2 bathymetric database. This data can also be used as bathymetric data for computational grids.

View Open Boundary Database

This option allows the user to visualize global gridded tidal harmonics databases and global harmonics at coastal locations. This data can be used as open boundary conditions for hydrodynamic simulations.

- 43 -

7. Grid Menu
This menu allows the user to generate computational grids for use with the hydrodynamic and mass transport models. See the getting started manual for more detailed information and instructions.

- 44 -

7. Run Model Menu

Run Hydrodynamic Model
Run Control
Start Time this is the time the hydrodynamic simulation is to start at. Interval for Currents Time Series (min) the duration of time between the currents time series in minutes (i.e. if 10 entered then the model will simulate currents every 10 minutes in the time series). Interval for Currents Field Output (min) the duration of time between the currents field output in minutes (i.e. if 10 entered then the model will predict currents every 10 minutes for the currents field output). Current Field Output there are two options the output can be time dated started with the entered start time or the current field can by a cyclical output current file. Make output for water quality model -This box must be checked if mass transport simulations will be conducted using the hydrodynamic simulation. The mass transport simulations require auxiliary files that can be large and are unnecessary if no such simulations will be conducted. Surface Boundary Forcing Options -This option allows the user to select wind files or environmental data such as solar radiation if complex simulations are to be conducted. See the on-line help for file type specification and use details.

Model Parameters
Number of Z Grids This controls the number of vertical layers in a simulation. For example 1 layer would be a two-dimensional simulation while more than 1 layer would be a three-dimensional simulation. Time Step (min) The numerical time increment at which the model runs. Ramp Time Period (min) This controls a cosine ramp of the open boundary conditions. It is necessary so as not to shock the system at a beginning of a simulation. Ramp for Wind (min) - This controls a cosine ramp of the wind surface condition. It is necessary so as not to shock the system at a beginning of a simulation. Residual Start Time (min) The time after which a simulation has started that the algebraic current residual will be calculated. Processes The check boxes in this section determine if salt and temperature transport will be conducted and if so if it will be as a conservative tracer or in baroclinic mode. This should only be used for very sophisticated modeling applications.

- 45 -

Smoothing Parameters Allows the user to smooth both bathymetry and currents during a simulations period if desired.

Physical Parameters
Wind Drag Coefficient The wind drag coefficient is a dimensionless parameter used to scale the calculation of the tangential stress at the ocean surface. WQMAP uses a quadratic wind stress formulation with a constant wind stress coefficient. A typical value of the wind drag coeffieicent is on the order of 0.0014. Reference: Kowalik, Z. and T.S. Murty, 1993. Numerical Modeling of Ocean Dynamics. Pg. 26. Vertical Viscosity (m2/sec) The equations of motion (momentum) and continuity serve to describe the average distribution of velocity and density. This motion however is typically irregular and turbulent. The interaction of the the turbulent motion with the average motion in the vertical direction within WQMAP is described by the vertical eddy viscosity. WQMAP utilizes a constant vertical eddy viscosity formulation with avgerage values ranging from 0.0001 to 0.1 m^2/s. When three-dimensional simulations are conducted this term can be used to control the amount of vertical shear present in the current structure over the water column. Reference: Kowalik, Z. and T.S. Murty, 1993. Numerical Modeling of Ocean Dynamics. Pg. 28. Vertical Dispersion (m2/sec) Dispersion coefficients refer to terms in the conservation of temperature and salinity equations used within WQMAP. Dispersion coefficients are empirical analogs of the molecular diffusion coefficients defined in the traditional advection-diffusion equation. The vertical dispersion coefficient controls the exchange of substance (temperature or salinity) in the vertical direction. WQMAP utilizes a constant vertical dispersion coefficient formulation with typical ranges of 0.000001 to 0.0001 m^2/s. Most esturarine applications can be started with a value of 0.001 m^2/s. Reference: USEPA, 1990. Technical Guidance Manual for Performing Waste Load Allocations, Book III, Part 2 Application of Estuarine Waste Load Allocation Models Horizontal Dispersion (m2/sec) Dispersion coefficients refer to terms in the conservation of temperature and salinity equations used within WQMAP. Dispersion coefficients are empirical analogs of the molecular diffusion coefficients defined in the traditional advection-diffusion equation. The horizontal dispersion coefficient controls the exchange of substance (temperature or salinity) in the horizontal direction. WQMAP utilizes a constant horizontal dispersion coefficient formulation with typical ranges of 0.01 to 10 m^2/s. Most esturarine applications can be started with a value of 1 m^2/s. Reference: USEPA, 1990. Technical Guidance Manual for Performing Waste Load Allocations, Book III, Part 2 Application of Estuarine Waste Load Allocation Models Temperature/Salinity Initial Conditions a constant or grid value can be used. False Bottom If the flooding and drying module is not available then this value should be set on the order of the expected tide range to minimize the potential for numerical instability. Bottom Boundary Condition This value refers to a quadratic bottom stress coefficient which represents frictional forces.

- 46 -

Run Mass Transport Model

Start Time this is the time the mass transport simulation is to start at. Run Length (days) the duration of time to run the mass transport model in days. Concentration Output Start time for concentration output Interval for Concentration Time Series (min) the duration of time between the concentrations time series in minutes (i.e. if 10 entered then the model will simulate concentrations every 10 minutes in the time series). Interval for Concentration Field Output (min) the duration of time between the concentrations field output in minutes (i.e. if 10 entered then the model will predict concentrations every 10 minutes for the currents field output).

Model Parameters Number of Z Grids - This controls the number of vertical layers in a simulation. For example 1 layer would be a two-dimensional simulation while more than 1 layer would be a three-dimensional simulation. Time Step (min) The numerical time increment at which the model runs Load Ramp Time Period (min) - This controls a cosine ramp for the introduction of loads in the system being modeled. It is necessary so as not to shock the system at a beginning of a simulation Flushing Study This option allows the user to conduct numerical flushing studies. See WQMAP Getting Started Manual for more details and instruction.

Physical Parameters Vertical Diffusivity (m2/sec) The vertical diffusion rate of the mass being simulated. Horizontal Diffusivity (m2/sec) The horizontal diffusion rate of the mass being simulated. Decay Rate (1/day) The coefficient of an exponential decay rate for the mass being simulated. Settling Velocity (m/day) - The rate at which the mass being simulated settles in the water column.

- 47 -

Run Batch Mode

This lets the user run a series of scenarios right after the other without any user intervention. Batch mode can be run with all models. To do this, set up each scenario as you would to run the model normally but instead of selecting Run, select Save and Close. After all the scenarios are set up, from the Run Model menu select Batch Mode. Click on the box next to the scenario names that you would like to run, then select Go. The blue screen will pop up and all the selected scenarios will run one after the other.

Running a New Simulation

Please refer to the Getting Started Manual.

Viewing Trajectory Model Results

Please refer to the Getting Started Manual.

- 48 -

8. Model Output
View Time Series Data
Displays the currents (or concentrations) output at the time series locations in a graphical form. See WQMAP Getting Started Manual for more details and instruction.

Section View
This allows you to view the currents or concentrations in 3D. You can view each layer, from the side of a slice through the water column. To do this select Cross Section from the Model Output menu. Then select Section Line and draw a Line (clicking the left mouse key several times) for where you would like to view the output in 3D. The series of line segments need not be a straight line. Note that the first segment of the line drawn always is displayed on the left, with the final segment on the right end of the cross-sectional window.

Environmental Windows
Displays boundary condition data.

Export Time Series Data

Exports time series data as an ASCII file format.

Export Multiple Time Steps to Shape File

Exports current (or concentration) field data as a shape file.

- 49 -

9. Tools Menu
Deleting Scenario Files
To delete unwanted files created by WQMAP, select Delete Files from the Tools menu. This brings up the File Maintenance window. Select the type of file to be deleted and all existing files of that type will be listed for the active geographic location. From the list select the file to be deleted and then click on the Delete File button. You will be asked to verify that you really want to delete the selected file.

Importing/Exporting GIS Files

A variety of file formats may be imported into and exported from the WQMAP GIS. These files include TIE files (ASA ASCII format for GIS transfer), MIF/MID files (a standard ASCII format defined by MapInfo and used by many applications), SHP files (ArcInfo/ArcView binary shape files), and MOS files (an ASCII file format used by the US Dept. of Interiors MOSS public domain GIS). All geographic coordinate data are generally assumed to be in degrees of longitude and latitude, though WQMAP does support alternative formats for some file types. The format for TIE files is supplied in the appendix. The MIF/MID file format is available from MapInfo, and the Shape file format is available from ESRI. To perform any of these operations, select Import/Export Files from the Tools menu. From the Layer Import/Export dialog, select the operation that you wish to perform. At the top of the Layer Import/Export dialog are four options for map units: Lat/Lon, UK Coordinates, UTM, and Australian coordinates. All data in WQMAP GIS layers and base maps are stored in degrees latitude and longitude. All file export functions will write files only in degrees latitude and longitude. The file import functions can read and import files in either degrees latitude and longitude or in UTM coordinates. If you are importing data in UTM coordinates you must select the UTM option and then specify the following parameters: The UTM Zone The Datum False Easting False Northing Once this information is supplied, click on Close and continue the file import.

- 50 -

TIE Files
To export a TIE file: 1. Select Import/Export Files from the Tools menu. 2. Select the GIS layer to export. 3. Select the Layer to TIE Export option. 4. In the text field (lower right) specify a name for the TIE file (or leave the default name). 5. Select the directory where this file will be placed. 6. Click on the Export button to export the layer to the TIE file. To import a TIE file: 1. Select Import/Export Files from the Tools menu. 2. Select the TIE to Layer Import option. 3. Select a TIE file to import. 4. Select the layer that you wish to import to. 5. Click the Import button to import the TIE file to the selected layer. For TIE file import, the TIE file data is appended to the selected layer. To put the data on a new layer, click on the Add New Layer button and a new layer will be created. Then import the TIE file to this layer.

- 51 -

MIF/MID Files
To export to MIF/MID files: 1. Select Import/Export Files from the Tools menu. 2. Select the Layer to MIF/MID Export to export a GIS layer, or BDM to MIF/MID to export a base map. 3. Select the layer or base map to export. 4. In the text field (lower right) specify a name for the MIF file (or leave the default name). 5. Select the directory where this file will be placed. 6. Click on the Export button to export the layer to the MIF file. The geographic portion of the data will be exported to the MIF file; the attributes associated with each object will be exported to the companion MID file. To import MIF/MID files: 1. Select Import/Export Files from the Tools menu. 2. Select the MIF/MID to Layer Import to import a Mif/Mid to a new GIS layer, or MIF/MID to BDM Import to import a Mif/Mid to a base map (BDM file) for this geographic location. 3. Select a MIF file to import. 4. If importing to a layer, a layer does not need to be selected as the MIF/MID import will automatically create a new layer. This new layer will be created with a Microsoft Access database structure as defined in the MIF file. The attribute data for each geographic object will be imported from the MID file to the Access database. Drawing attributes such as color, symbol, and pen width are not imported; default values are used.

ESRI ArcView/ArcInfo Shape Files

To import SHP files: 1. Select Import/Export Files from the Tools menu. 2. Select the SHP to Layer Import option. 3. Select a SHP file to import. 4. You do not need to select a layer to import to. The SHP file import will automatically create a new layer. This new layer will be created with a Microsoft Access database structure identical to that in the associated DBF file (each SHP file should have an

- 52 -

associated DBF file which contains the object attribute data). The attribute data for each geographic object will be imported from the DBF file to the Access database. To export to SHP files: 1. Select Import/Export Files from the Tools menu. 2. Select the Layer to SHP Export option. 3. Select the layer to export. 4. Select the object type (points, lines, or polygons) to export. 4. In the text field (lower right) specify a name for the SHP file (or leave the default name). 5. Select the directory where this file will be placed. It is also possible to attach SHP files as a layer instead of importing them to WQMAP's layer format. When a SHP file is attached, WQMAP will draw the SHP file in its native format. See Attaching External Files to GIS Layers for more information.

MOS Files
The MOS file import reads an ASCII format file into an WQMAP GIS layer. 1. Select Import/Export Files from the Tools menu. 2. Select the MOS to Layer Import option. 3. Select a MOS file to import.

Converting 16-bit layers to 32-bit layers

1. Select Import/Export Files from the Tools menu. 2. Select the 16-bit Layer to 32-bit-Layer option. 3. Select a 16-bit layer to convert 4. In the text box, specify a name for the new 32-bit layer, or leave the default name. 5. Specify the directory in which the new layer will be placed.

Color Keys/Legends
Color keys are used in WQMAP to explain what different colors within a GIS layer or model grid cell represent. Keys can be easily created and edited.

- 53 -

Existing color keys may be opened under the Tools->Open Color Key menu. From this dialog, choose a key file (.kew) to open. Once a key is open it can be positioned on the screen by clicking on the caption bar at the top of the key, holding down the left mouse button and dragging the key to a new location. To modify a color key, bring up the Legend Editor by double-clicking on the color field of the key. The Legend Editor allows the user to: Set key titles Set each divisions name and color Automatically subdivide a range of values. Automatically apply a color ramp to a value range. Enter new key titles or edit existing titles by clicking in the title field and typing text. Click New Division to add a new division. Double-click on an existing division to delete the division. You may open existing color combinations and save new ones with the Open Color File and Save Color File buttons. You may also open existing divisions and save new ones with the Open Key File and Save Key File buttons. The Auto Division button allows you to create divisions between an entered maximum and minimum range arithmetically or logarithmically. The Color Ramps button allows for a selection of color ramps and the ability to invert the color order.

Leaving the first value in the first line blank (e.g., ;1.0) will create a lower range that is specified as less than the value in that line (<1.0). Leaving the second value in the last line blank (e.g., 100;) will create an upper range that is greater than the value in that line (>100). When the user right clicks on a field will allow you to add or delete fields. Once all changes have been made to the key, click OK to close the Legend Editor and save the key file.

Add Labels
Text labels may be placed on the map as annotation. Select Add Label from the Tools menu and draw a box on the map window in which to enter the text. Click in the text box and enter the desired text. When the text box is selected, it may be resized or moved with the mouse. When it is unselected (click anywhere else on the map window), right-clicking on it will bring up the options to remove the label or to reset label properties. Editable properties include background color and the font characteristics. Labels will automatically be removed from the map window when WQMAP is exited.

Export Grid to Mif/Mid file

This option exports the computational grid used in the simulation directly to a MIF/MID file.

- 54 -

10. Tides & Currents

If the Tides & Currents system (from Nautical Software, Nobeltec Corporation) is installed on your PC, then the Tides&Currents tab will be available.

View Tide Station Information

The View Tide Station Information option allows the user to create a layer that contains the specified tidal station locations and associated data. The search radius can be changed to find all the data stations in a given area around the area of interest.

View Current Station Information

The View Current Station Information option allows the user to create a layer that contains the specified tidal station locations and associated data. The search radius can be changed to find all the data stations in a given area around the area of interest.

- 55 -

11. Help
The help menu links to a series of help files: Getting Started Helpful documentation that lists step by step on how to create grids and scenarios. A complete description on how to interpret and view results is included. File Types documentation on all file types that WQMAP requires as input and that it outputs. Technical Manual documentation that contains the algorithms that the WQMAP system uses. About WQMAP this informs what version of WQMAP that you are currently working with.

- 56 -

12. Frequently Asked Questions

1. The program says that it can't find my hardware key, why? Most installations of WQMAP are delivered with a Hardlock key, which is required to run the program. The key should be plugged into the computers parallel (printer) port whenever you use WQMAP. The installation program should run the Hldrv32.exe program that tells the computer how to interface with the key so that the operation is essentially seamless. 2. How do I import GIS data from ArcView? GIS data created as ArcView Shape (SHP) files may be either imported to a new GIS layer, or attached, as a SHP file, to a GIS layer. To import a SHP file: Select Import/Export Files from the Tools menu Select the SHP to Layer Import option. Select a SHP file to import. The SHP file import will automatically create a new layer. This new layer will be created with a Microsoft Access database structure identical to that in the associated DBF file (each SHP file should have an associated DBF file which contains the object attribute data). The attribute data for each geographic object will be imported from the DBF file to the Access database. Alternatively, you may attach a Shape file. Select Attach New Layer from the GIS menu. Select ArcView Shape File and the file that you wish to attach. When Shape files are attached, no conversion or import is performed; WQMAP simply draws the shape file in its native format. Drawing attributes such as color and icon may be specified as for any other layer. 3. How do I import data from Mapinfo? A variety of file formats may be imported into and exported from the WQMAP GIS. This includes MIF/MID files, a standard ASCII format defined by MapInfo and used by many applications. To import MIF/MID files: Select Import/Export Files from the Tools menu. Select the MIF/MID to Layer Import to import a Mif/Mid to a new GIS layer, or MIF/MID to BDM Import to import a Mif/Mid to a base map (BDM file) for this geographic location. Select a MIF file to import. The import will automatically create a new layer, which will be created with a Microsoft Access database structure as defined in the MIF file. The attribute data for each geographic object will be imported from the MID file to the Access database. Drawing attributes such as color, symbol, and pen width are not imported; default values are used. 4. I want to use a different base map in my location, how do I do this? The base map in WQMAP displays the land and water features for the active geographic location. Base maps can be created from one of many vector or raster file formats. Change the base map displayed in the current geographic location by choosing Base Map from the File menu, select a file type and the disk drive and directory where the file exists, and then highlight the file to be used. The selected base map will be active in the current geographic location until a different file is selected. If you have a base map in MapInfo Mif/Mid format that you wish to use, it may be imported as a BDM file (ASA base map format) by selecting Import/Export Files from the Tools menu. 5. What do "raster" and "vector" mean? The base map in WQMAP displays can be created from one of many vector or raster file formats. Vector base maps consist of polygons depicting the land features within an area. When drawn in the map window, the land polygons are drawn in one color (e.g. green) on a background of a

- 57 -

different color (e.g. blue). Raster base maps are bitmaps created by scanning a paper map into digital form. A raster base map captures all the features on the paper map and creates a fixed image of the map. 6. Can I use a raster map? WQMAP is available with raster support. Two raster base map formats (BSB Electronic Charts, and Resolution Mapping/Maptech) are commercially available on diskette for single charts or on CD-ROM for all charts within an entire region. These charts are available at most nautical supply stores. WQMAP can also use georeferenced TIF (GeoTif) files. A version of WQMAP is also available that supports British Admiralty Raster Charts (ARCS).

- 58 -

Appendix

- 59 -

Appendix A: Directory Structure, Input and Output Files

Directory Structure
\WQMAP \ICONS \LOC.DATA \location (ex. STARTING) \COAST \CURRENTS \GIS \GRIDS \ICONS \KEYS \LOADS \OUTMASS \OUTWASP \RUNHYDRO \RUNMASS \RUNWASP \TIMESERIES \WATERSHEDS \WINDS \SYSTEM

executables system default GIS icons geographical locations coastline map data hydro model output GIS data model grid location specific GIS icons location specific color key data mass and WASP model load GIS data mass transport model output files eutrophication model output files hydro scenario input files mass transport scenario input files eutrophication model scenario input files model time series GIS data runoff model input watershed data wind data WQMAP system and default

A- 1

HYDRO Input Files

\RUNHYDRO directory Scenario.BFH* Scenario.DGS* Tidefile.HST Scenario.OBD* Scenario.RIV* Riverfile.RVR Scenario.VEN *Made by the WQMAP interface \GIS directory Tsrfile.TSL* \GRIDS directory Gridfile.DGR * \TIMESERIES directory Tsrfile.GDP* Tsrfile.GDW Tsrfile.LIN
* * * *

Model runtime control Salinity, temperature and bottom friction field initialization data Open boundary elevation,salinity & temperature time series Tidal open boundary specification River boundary specification Variable river flow data Intake/outfall recirculation specification

Output time series locations

Boundary fitted grid

Output time series locations Output time series locations Output time series locations Output time series locations Output time series locations

Tsrfile.LOK

Tsrfile.MDB

\WINDS directory Windfile.WNE * Windfile.WNV

Wind time series Atmospheric and solar data

A- 2

HYDRO Output Files

\CURRENTS directory Scenario.BFH Scenario.BFU Scenario.BPC Scenario.DGR Scenario.ENV Scenario.ERG Scenario.FLO Scenario.HCF Scenario.K... Scenario.OBD Scenario.PRF Scenario.PRT Scenario.RES Scenario.RIV Scenario.RWW Scenario.SMB Scenario.SRF Scenario.STC Scenario.STR Scenario.TSA Scenario.TSC Scenario.TSL Scenario.TSP Scenario.TSQ Scenario.UVC

Scenario.VEN Scenario.XSC Scenario_TS.GDP Scenario_TS.GDW Scenario_TS.LIN Scenario_TS.LOK Scenario_TS.MDB

copy of input plot control Current vector output for viewing copy of the grid environmental data (plotting) energy balance data Volume flow data surface heat balance data plotting keys copy of open boundary data vertical profile data for debug output log file current residuals copy of constant river input variable river input salt mass balance data surface heat exchange terms salinity/temperature data restart file ASCII output for debug time series output for plotting time series locations data Volume flow time series data: I-dir Volume flow time series data: J-dir Current/salinity/temperature output for BFMASS and BFWASP heat source data Time series output data for plotting Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data

A- 3

MASS Input Files

\CURRENTS directory Scenario.UVC* \GIS directory

Current/salinity/temperature input Output time series locations

Tsrfile.TSL*

\GRIDS directory

Gridfile.DGR *

Boundary fitted grid

\LOADS directory

Loadfile.GDP* Loadfile.GDW* Loadfile.LIN* Loadfile.LOK* Loadfile.MDB*

Output time series locations Output time series locations Output time series locations Output time series locations Output time series locations

\RUNMASS directory Aslfile.ASL Scenario.BFM* Loadfile.LOA* Scenario.MBD*

Time dependent load specification Model runtime control Load specification master file Open boundary specification Special model control data Output time series locations Output time series locations Output time series locations Output time series locations Output time series locations

Wq_model.PRM
\TIMESERIES directory Tsrfile.GDP*

Tsrfile.GDW Tsrfile.LIN* Tsrfile.LOK* Tsrfile.MDB*

A- 4

MASS Output Files

\OUTMASS directory Aslfile.ASL Scenario.BFM Scenario.DGR Scenario.K* Loadfile.LOA Scenario.MAS

Copy of time dependent load specification Copy of model runtime control Copy of model grid Scenario specific color keys Copy of load specification master file Concentration output data Copy of open boundary specification Concentration maximums output data Output log file Sediment mass output data Time series location data Time series output data Time series output data for plotting Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data Copy of time series GIS data Copy of load file GIS data Copy of load file GIS data Copy of load file GIS data Copy of load file GIS data Copy of load file GIS data

Scenario.MBD Scenario.MXM Scenario.PRT Scenario.RCT Scenario.SED Scenario.TFG Scenario.TSL Scenario.TSM Scenario.XSM Scenario_TS.GDP Scenario_TS.GDW Scenario_TS.LIN Scenario_TS.LOK Scenario_TS.MDB Scenario_Lo.GDP Scenario_Lo.GDW Scenario_Lo.LIN Scenario_Lo.LOK Scenario_Lo.MDB

A- 5

GRID Input Files

\GRIDS directory Gridfile.ADD

Depthfile.DPT Gridfile.INP *

Constant depth offset ASCII depth data Boundary fitted grid

GRID Output Files

\GRIDS directory Gridfile.AGR*

Gridfile.DGR* Gridfile.PRT* Depthfile.LOG*

ASCII boundary fitted grid Boundary fitted grid used by models Grid generation model log file Depth gridding model log file

WQMAP Executables
\WQMAP directory WQMAP.EXE BFGRID.EXE ORTHOHYDRO.EXE ORTHOMASS.EXE ORTHOWASP.EXE DEP_GRID.EXE

Main WQMAP98 program Boundary fitted gridding model Hydrodynamics model Mass transport model Eutrophication model Depth gridding model

A- 6

Appendix B: ASCII File Formats

Wind File Format - *.ASW
Below is the format used to create a wind file based on ascii data. The file is to have the *.asw extension and be located within the wind sub-directory. The file can be either used directly into the hydrodynamic model or can be converted into a *.wne (binary file) using the wind editor. Line # 1 2 3 4 5 6 7 8 9 Description Station latitude N or S Station longitude E or W Description of data Start year month day hour End year month day hour Station height units of measurement (knots or m/s) End year month day hour meteorological direction speed Variable Decimal degrees Decimal degrees Optional; can be blank Space delimited Space delimited Format Real*4 Character*1 Real*4 Character*1 Character*80 Integer*2 Integer*2 Integer*2, character*5 Integer*2

Example 53.4144134521484 N 5.50178252160549E-03 W DEMONST.WNE 96 3 9 7 96 3 11 15 10 KNOTS 96 3 9 7 22 15 96 3 9 8 22 15 96 3 9 9 68 15 96 3 9 10 68 15 96 3 9 11 112 15

B- 1

A Single Load Constituent File - *.ASL

Below is the format used to create a single load (ASL) constituent file, used as a time based release within the BFMASS and BFWASP model. The file must have the *.asl extension and be placed in the LOADS subdirectory. The example attached shows how to set up an intermittent load that starts and stops every 24 hrs. The first few lines follow: 2: 5: 27: 1995 1995 1995 1995 1995 1995 1st line - Load type =2 = time dependent load rate 2nd line - Constituent#=5 (See list below) 3rd line - number of times to follow=27 in the example file 03 03 00 00 00 0.00 : Yr Mo Dy Hr Mi Sec Load (Mass/sec) - 1st time 03 03 01 00 00 86400.00 : Yr Mo Dy Hr Mi Sec Load (Mass/sec) - 2nd time 03 03 02 00 00 0.00 : ... 03 03 23 00 00 0.00 03 04 00 00 00 86400.00 03 04 01 00 00 0.00

Constituent # 1. Ammonia 2. Nitrate 3. Inorganic Phosphorus 4. CBOD 5. Dissolved Oxygen 6. Organic Nitrogen 7. Organic Phosphorus 8. Non reacting Chemical 1 9. Non reacting Chemical 2 The ASL file is attached to a load by selecting the ASL file button on the load edit form and selecting the chosen ASL from the list in the drop down menu. You can arrange the times to turn on and off at any interval the increment between times does not need to be constant. But note that the model will linearly interpolate between time steps.

B- 2

Depth Import File Format - *.DPT

A simple ASCII formatted file (lon lat depth) for use with a boundary fitted coordinate grid. The data can be either comma or space delimited. The file is must have a *.dpt extension and be located within the grids sub-directory. An example of the file format is provided below: -117.196 32.67956 -117.192 32.67913 -117.186 32.67935 -117.183 32.67902 -117.171 32.6788 -117.169 32.67865 -117.163 32.67915 -117.154 32.67889 -117.148 32.67897 -117.143 32.67863 -117.139 32.67839 -117.134 32.67828 -117.118 32.60075 -117.12 32.60275 -117.118 32.60336 -117.122 32.60451 -117.12 32.60511 -117.118 32.60512 -17.124 32.60746 1.0 22 27 25 20 17 16 10 7 12 11 28 36 1.0 1.0 3.5 2.5 2.5 1.5

B- 3

Atmospheric File Format - *.WNV

The *.wnv file is an atmospheric file based on ascii data, to be used for prognostic simulations. The file must have the *.wnv extension and be located within the winds sub-directory. Line # 1 2 3 4 5 6 7 8+ Description Station latitude E or W Station longitude N or S Start year month day hour minutes End year month day hour minutes Header information as shown below Data Variable Decimal degrees Decimal degrees Space delimited Space delimited Format Real*4 Character*1 Real*4 Character*1 Integer*2 Integer*2

An example of the file format is provided below: 71.3 W 41.75 N

1997 1997
Yr

12 12

1 16

1 18

00 00
Solar Radiation (W/m^2)

Air Dew Pt Relative Tmp Tmp Press Humidity W-E W-N Mo Dy Hr Mi ( C) ( C) mBar (%) m/s m/s

1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12 1997 12

01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01 01

00 00 01 00 02 00 03 00 04 00 05 00 06 00 07 00 08 00 09 00 10 00 11 00 12 00 13 00 14 00 15 00 16 00 17 00 18 00 19 00 20 00 21 00 22 00 23 00

1.67 1.11 1.11 1.11 0.56 -0.56 0.00 -0.56 1.11 2.78 4.44 6.11 6.11 7.22 7.22 7.22 6.11 4.44 4.44 2.78 1.11 0.56 0.00 -0.56

-3.89 -3.89 -3.89 -3.89 -3.89 -3.89 -3.89 -3.89 -3.33 -3.33 -4.44 -4.44 -5.00 -5.56 -6.67 -7.22 -7.22 -6.67 -7.22 -6.67 -6.11 -6.11 -5.56 -5.56

1019.98 1019.98 1021.00 1021.33 1021.67 1022.01 1022.69 1023.37 1024.38 1024.72 1025.40 1025.06 1024.72 1024.38 1024.38 1024.72 1025.06 1025.74 1026.41 1026.41 1026.75 1027.09 1026.08 1025.74

0.66 4.79 0.69 3.42 0.69 4.40 0.69 4.11 0.72 4.65 0.78 2.71 0.75 3.48 0.78 2.71 0.72 2.40 0.64 2.01 0.52 2.68 0.46 0.93 0.44 2.14 0.39 0.93 0.36 3.08 0.35 4.65 0.37 3.48 0.44 1.56 0.42 1.72 0.50 2.94 0.58 3.52 0.61 2.74 0.66 2.52 0.69 3.36

-4.02 -2.87 -0.78 -3.45 -2.68 -1.56 -2.01 -1.56 -2.01 -2.40 -4.65 -5.28 -5.88 -5.28 -0.54 -2.68 -2.01 -2.71 -2.05 -1.07 -0.62 -2.30 -0.92 -1.22

0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 22.89 156.17 298.29 395.89 433.89 366.49 287.36 164.31 36.60 0.00 0.00 0.00 0.00 0.00 0.00 0.00

B- 4

Open Boundary Tidal Forcing File - *.HST

The HST file is a time series file for tidal forcing, salinity and temperature to be linked to the open boundary cells. It is a simple ASCII format year, month, day, hour, minutes, elevation (m), salinity (ppt) and temperature (oC). The data can be either comma or space delimited. The file is must have a *.hst extension and be located within the runhydro sub-directory. An example of the format is provided below: line 1: must have a default header - Version= Version= 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3 4 4 0 15 30 45 0 15 30 45 0 15 30 45 0 15 30 45 0 15 -0.400 -0.330 -0.230 -0.140 -0.040 0.070 0.180 0.300 0.410 0.520 0.630 0.740 0.840 0.930 1.020 1.090 1.150 1.200 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 2

B- 5

River Boundary Discharge File - *.RVR

The RVR file is a time series file used to replicate the river discharge, which is to be linked to the river cells. It is a simple ASCII file that can be either comma or space delimited. The file is must have a *.rvr extension and be located within the Runhydro sub-directory. An example of the file formal is provided below: Line 1 must have a default header - Version= 2 Line 2:- as shown below Version Y 1997 1997 1997 1997 1997 1997 1997 =2 M 6 6 6 6 6 6 6 D 1 1 1 1 1 1 1 H 1 2 3 4 5 6 7 Min 0 0 0 0 0 0 0 Flow(m3/s) Temperature(C) Salinity(ppt) 249.82 26 0 250.13 26 0 250.45 26 0 250.76 26 0 251.06 26 0 251.69 26 0 252 26 0

B- 6

Appendix C. TIE Format for GIS Data Import/Export

The TIE file is an ASCII format used for exporting and importing map information contained in WQMAP GIS layers. To import map data to a layer, assemble the data in an ASCII file using the TIE format and import using the IMPORT/EXPORT FILES command found in the TOOLS menu. Data definition for TIE file. line no. content format comments ------------------------------------------------------------------------------------------------------------1 2 3 4 ID number name description POINT LINE POLYLINE POLYGON color width height color width height color width height pcolor bcolor pattern icon name (i.e. RECTANGLE) layer number attribute(1) attribute(2) attribute(3) attribute(4) attribute(5) attribute(6) link file name real number number of vertices x y (I*2) (c20) (c20) unique identifier object name description data field object type object type object type object type if point object if line object if polyline object if polygon object values 1-50 (any text information attached to object)

6 7 8 9 10 11 12 13 14 15 16 17

(3i3) (3i3) (3i3) (3i3) (i*2) (c40) (c40) (c40) (c40) (c40) (c40) (c40) (real*4) (i*2) (2f14.6)

PCX, GRF, TXT (any real number associated with object) (i.e., 1 for points 2 for lines, 1-x for polylines/polygons) longitude, latitude Positive East & North Negative West & South

C- 1

Appendix D. How to create base maps, process large polygon layers and work with GIS layers and SHP files
Managing GIS Data in SHP Files
ArcView GIS uses the SHP file as its native file format for storing GIS data. Using the ASA GIS system one can use data in SHP files in two ways. The first way is to establish a link to an existing SHP file so that it becomes the source for a GIS layer or base map in the model system. The second method is to read the contents of a SHP file and convert it into an ASA GIS layer or model system base map. When working with SHP files in the ASA model system GIS it is important to be aware of specific requirements regarding the size and nature of GIS objects that can be stored in SHP files and ASA GIS layers, as well as the coordinate system used to store the objects. This document provides guidelines for working with GIS data in SHP files and discusses the advantages and disadvantages of the attaching versus import methods used to bring GIS data into the ASA model systems.

SHP Files
A SHP file stores the geographic features of a map layer as points or as the vertices of a polyline or polygon. SHP files will always have at least two companion files: the DBF file and the SHX file. The DBF file is a standard dBase file with one record for each geographic feature in the SHP file. This file holds all the attribute data associated with the related geographic feature. The SHX is an index file containing one record for each geographic object in the SHP file. The records in the SHX contain a pointer to the location of the object within the SHP file. All three files must have the same name. For example, a layer containing mangrove distribution data might be stored in the files Mangrove.shp, Mangrove.dbf and Mangrove.shx. SHP files can store geographic feature data in many different coordinate systems and map projections. The ASA model system GIS uses only geographic coordinates (degrees latitude and longitude) for all map features. All SHP files attached to or imported

into the ASA GIS must use geographic coordinates.

Limits Imposed by the Operating System

Each of the Microsoft operating systems has a limit to the number of vertices that each polygon in a GIS layer can contain. Windows 95/98 is a 16-bit operating system and is limited to 32,767 points in a single polygon. Windows NT/2000 is a 32-bit system and can handle more than 4 billion points in a single polygon. When a polygon exceeding these limits is either attached or imported into the ASA GIS no errors will occur, but any polygons exceeding the vertex limit will not display on the map. To solve this problem, large polygons can be subdivided so that they do not exceed the limitations imposed by the operating system. Use the Intersect function in ArcInfo or in the Geoprocessing Wizard extension in ArcView to subdivide large polygons and get around the vertex limits. A brief discussion of the intersection process is given later in this Appendix. Refer to the appropriate ArcInfo or ArcView documentation for details.

GIS Layers

D- 1

The ASA model system GIS can have an unlimited number of map layers. These map layers can be created using the GIS interface or by attaching to or importing external GIS files.

Attaching SHP Files as GIS Layers

Attaching directly to an existing SHP file is an easy way to add a layer to the ASA GIS. When a SHP file is attached in this way it becomes the source for the layer. The advantages of using this method are that no file conversion has to occur and the model system GIS and ArcView share the same source files. The disadvantage of attaching to a SHP file is that the model system GIS can not be used to edit the layer or to assign colors and fill patterns to individual layer objects. When an attached layer is the active layer, the layer edit tools will be deactivated and no changes can be made to the layer. Refer to the User Manual for a description of how to attach a SHP file as a GIS layer.

Importing SHP Files into GIS Layers

In many instances it is desirable to import a SHP file into the ASA GIS so that the layer can be edited. When a SHP file is imported, the contents of the file are converted into a new set of files that become the source for the layer. This layer is fully editable in the model system GIS. New point, line and polygon objects can be added to the layer and existing features can be edited. Refer to the User Manual for a full description of how to import a SHP file into a GIS layer.

Base Maps
The ASA model system GIS uses a fixed base map for each geographic location that is always displayed in the map window. Each geographic location has a default base map file named Landpoly.bdm, but additional base maps can easily be created within a location. The base map should only contain polygons representing land, all other space on the base map layer is assumed to be water.

Attaching SHP Files as Base Maps

New base maps can be created simply by attaching directly to a SHP file. The features in the SHP file must be stored in geographic coordinates. If the SHP file has been created using a projected coordinate system, create a new SHP file using geographic coordinates before attaching it as a base map. Also, make sure that only polygons representing land are included in the SHP file. Follow the directions in the User Manual for attaching a SHP file as a base map.

Importing SHP Files into a Base Map

New base maps can also be created by importing a SHP file into the ASA GIS base map file format. The SHP file must use geographic coordinates (degrees latitude and longitude), must only contain polygons representing land features, and must not contain any polygons with holes. Refer to the User Manual for details on how to create a base map by importing a SHP file.

Performing the Intersection of two Polygon Layers

The intersection between two GIS layers results in a third layer that is a combination of the features in both input layers and covers the area common to both input layers. This discussion will focus on using the intersect process to create a new polygon layer with

D- 2

polygons that do not exceed the maximum number of vertices allowed for a single polygon. Figure 1 and the text below explain the intersect process: 1. Create a new layer, add a rectangle to the layer that encloses all of the features in the polygon layer that is to be subdivided. Subdivide the rectangle in the new layer to form smaller adjacent rectangles with shared borders (polygon grid layer in Figure 1). 2. Using the new grid layer and the layer containing the large polygons, use the intersect function to generate a third layer with sub-divided polygons.

Figure 1. The intersection of two GIS layers results in a third layer that combines the features of the input layers and covers the area common to both. This process is available in ArcInfo and in the Geoprocessing Wizard extension in ArcView. No attribute information is lost in the output layer and the spatial extent of the output layer is the area common to the two input layers. The intersect process is explained in detail in the ArcInfo and ArcView on-line help. The Intersect function is only available in ArcView if the Geoprocessing Wizard extension is loaded into the ArcView project.

D- 3

Appendix E: Helpful Websites to determine Environmental Data

Metrological Data
National Climatic Data Center (2003). http://lwf.ncdc.noaa.gov/oa/ncdc.html. This website can be used to search for weather information, such as precipitation, minimum and maximum daily temperature, and wind speed and direction, for a particular weather station. The user can search for station by state, city, zip code, country or other ID codes. These data need to be purchased, however, at a low cost (e.g. $2.00/day). NOAA Center for Operational Oceanographic Products and Services (CO-OPS, 2003). http://www.co-ops.nos.noaa.gov. This website allows user to retrieve meteorological and oceanographic data for various NOS data collection platforms (DCP) or ports. Use the station locator link to find the stations in the area of interest. Data available at this site include air temperature, water temperature and wind speed, direction and gusts. These data can be downloaded at no charge. National Data Buoy Center (2003). http://www.ndbc.noaa.gov/. This website allows user to download recent and historical wind and standard meteorological data from moored buoys and C-MAN stations across the country. Start by clicking on the box of the area of interest. These data are available for download at no charge.

Bathymetric Data
National Geophysical Data Center (NGDC), GEODAS Inventories (2003). http://www.ngdc.noaa.gov/mgg/gdas/. This website allows user to search for and download bathymetric data for areas throughout the world. These data are available for download at no charge.

E- 1