2.05 SEDPAK LAUNCH and Other Menus and the SEDPAK Window
The description that follows in this section provides a very preliminary overview of the SEDPAK SIMULATION and its major menus. A much more detailed description of these menus is provided in the appropriate chapters and sections which are referred to below.
The GUI (Graphical user interface) or user interfaces for SEDPAK consists of the four major menus: the SEDPAK LAUNCH menu (Section 2.16), the SEDPAK EXEC menu (Chapter 4), the SEDPAK EDIT menu (Chapter 3), and the SEDPAK FACIES menu (Chapter 5); and the SEDPAK SIMULATION window which displays the graphical output of the execution of the SEDPAK .
Figure 2.5.1. The SEDPAK SIMULATION Window. Note that the last action performed with the EXEC menu, Zoom mode turned off, is recorded in the left basal portion of the window.
The SEDPAK LAUNCH menu (Figure 2.5.2) is invoked by typing sedpak at the command line prompt and pressing the return key. An icon menu appears with buttons which can be pressed to invoke the menus for the EXEC (refer to Chapter 4), EDIT (refer to Chapter 3), FACIES (refer to Chapter 5),overlay (refer to Section 2.17), Adobe (refer to section 2.07), Calculator, and the Help system (refer to Section 2.09). The Calculator button provides access to the X calculator, and Exit closes the icon menu, but does not close other menus and programs initiated from the icon menu. These other applications have to be closed from their respective menus.
Figure 2.5.2. The SEDPAK LAUNCH Menu.
The SEDPAK simulation execution is controlled by the EXEC, EDIT, and FACIES menus. Following loading a data (.db) file (Section 2.06), the SEDPAK SIMULATION window (Figure 2.5.1) displays the graphical output from the execution of SEDPAK. Displays are controlled from the SEDPAK EXEC menu, and include various basin cross sections (including Basin-Lithologic Ratio, Basin-Facies, Basin-Sequence and Basin-Maturity) a chronostratigraphic diagram, various well plots (Time-Depth-Elevation, Burial History, Geohistory, and Maturity history), the timing of the peak of oil generation for a kinetic model, and a sea level and sediment supply plot. All these displays, except sea level and sediment supply, can be viewed in one or two display windows, placed one above the other. Messages recording the most recent action performed with the EXEC menu are written at the bottom left of the window. This message helps keep track of the execution of the program and also records when inappropriate data is entered (see Section 2.13). At the bottom right are two small areas, designated X: and Y:, which display the vertical and horizontal positions of the mouse pointer on the current display, e.g. the basin cross section, well plot, chronostratigraphic diagram, and/or sea level/sediment supply graph.
Figure 2.5.3. SEDPAK EDIT menu
The SEDPAK EDIT menu (Figure 2.5.3) is activated to input the values for
the variables which are used by the program. These input parameters are
divided into logical groupings (Table 2.2.2) represented by selections on
the SEDPAK EDIT menu. and are described in Chapter 3 of this manual. Data
entry to these selections uses either dialogs, or combined plotters (Section 2.10) and data sheets (Section 2.11). Numerical data can be modified by means of calculators attached to each
data sheet (Section 2.12). Results of such calculations can be viewed in
graphical form on the plotters.
The SEDPAK EXEC menu (Figure 2.5.4) opens the SEDPAK simulation window and controls the manner in which the simulation output is viewed (see Chapter 4). To run the simulation, a data file (with .db as a suffix) is loaded by selecting Open from the File pull-down menu on the SEDPAK EXEC panel as described in section 2.06. Select a file from the file selection window and then click OK. Execution of the data (.db ) file will begin, with output from the simulation appearing in the SEDPAK SIMULATION window. Pressing Cancel will close the Open a File dialog without executing the file.
Figure 2.5.4. SEDPAK EXEC menu
The SEDPAK EXEC menu options include the Execution Controls, commands for pausing (Pause), resuming (Resume), loading and restarting (Load then Restart), and zooming (Zoom) the simulation. The Plotting Controls options manage the plotting times of the simulation output. Display Controls manages the number of surface lines that appear on simulation output. Display Modes provides access to the options menu which controls the type of output that is displayed and in which of the two potential windows. These displays emphasize different geological features, e.g.,
The various modes and options can only be selected when the simulation is
completed or paused by using the Pause button.
Pull-down and/or tear-off menus on the SEDPAK EXEC menu bar include File (see Section 2.06), Option (see Section 2.07), View (see Section 4.05) and Help (see Section 2.09). When File is pulled down from the SEDPAK EXEC menu, the options are Open, Pause, Resume, Load then Restart, Print Selection, Surface Snapshot, Close Simulation, and Quit.
1) Overlay on gif files of the basin stratigraphy and seismic cross section.
2) Manipulate to form unconformities.
3) Generate sediment layers for Out of plane Deposition.
The SEDPAK FACIES menu is for creating and editing facies files which can be attached to the file being currently executed by the SEDPAK EXEC (see Chapter 5). Clicking on the FACIES button or the launch menu activates the Sedpak Facies Editor (Figure 2.5.5). This has three pull-down menus located on the upper left of its menu bar. These are File, Facies, and Display. A Help button lies to the right hand end of the menu bar. The options on the File pull-down menu includes Open, Merge, Import, Save, Save As..., Close and Quit. A file is loaded for editing by selecting Open (see Section 2.06) which activates the dialog for retrieving a facies (.facies ) file. This file can be selected from the benchmarks facies (.facies ) file library, edited and saved. This can be with Save as the old facies (.facies ) file or with the Save As... option as a new facies (.facies ) file.
Figure 2.5.5 Sedpak Facies Editor window.
On the SEDPAK EDIT menu, the menu items with... activate pull-down menus which access cascade menu items. Additionally, on the SEDPAK EXEC and SEDPAK FACIES menus, ... indicates menu items which invoke other dialogs. The menu bars for the SEDPAK EDIT, the SEDPAK EXEC, and SEDPAK FACIES panels contain pull-down menus. On the SEDPAK EXEC menu, the pull-down menus are File, Option, View, Examine, and Help. On the SEDPAK EDIT menus, the pull-down menus are File, Option, Examine and Help. The use of the File, Option, Examine and Help menus are explained in the next three sections (Section 2.06, 2.07, 2.08 and 2.09) and the View menu is discussed in Chapter 4 on the EXEC panel in Section 4.05, View controls.
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2.06 The File Menu
File menus (Figure 2.6.1.) are available from the SEDPAK EDIT, the SEDPAK EXEC and the SEDPAK FACIES menus.
When File is pulled down from the SEDPAK EDIT menu, the options are Open, Close, Save, Save As, and Quit.
When File is pulled down from the SEDPAK EXEC menu, the options are Open, Pause, Resume, Load then Restart, Print selection, Surface Snapshot, Close Simulation, and Quit (see Chapter 4 for details except for Open and Print selection).
Close Simulation ends the current simulation and closes the SEDPAK SIMULATION window. The
SEDPAK EXEC menu remains active on the computer screen so that additional
files can be opened and executed.
Quit terminates the execution of the simulation, and the SEDPAK EXEC menu is closed.
When File is pulled down from the SEDPAK FACIES menu, the menu options are Open, Merge, Import, Save, Save As..., Close, and Quit.
Figure 2.6.1 shows the dialog which is displayed when Open is selected from the File pull down menus on either the SEDPAK EDIT or SEDPAK EXEC panels to load data (.db ) files. A similar dialog is also activated to "save" as well as load data (.db ), facies (.facies), surface (.sur), gif (.gif), postscript (.ps), and other files. In Figure 2.6.1, the current directory is /home/hickey/Ex4Man, as indicated in the Filter text area at the top of the dialog. Directories under the current directory are presented in the Directories list area to the left. Files with names ending in .db, as selected by the filter in the Filter text area, are presented in the Files list area on the right. A file is selected from the Files list by clicking the mouse button when the mouse pointer is over the name of the file to be selected. The Selection text area of the dialog in Figure 2.6.1 shows that the file PleisoAmoco.db has been selected from the Files list. Note that the full path name, as shown in the Selection text area, has been constructed by appending PleisoAmoco.db from the Files list to the prefix /home/hickey/Ex4Man shown in the Filter text area. At this point, clicking the OK button will cause the file which appears in the Selection text area to be read for execution or editing.
Figure 2.6.1. File Selection Dialog for
saving and loading files.
It is also possible to move to other directories. Typing the full path name
of another directory in the Filter text area and then pressing the Filter button will apply that filter and display the contents of the new directory
in the list areas. It is possible also to "navigate" around the directory
tree. For example, in the Directories scroll area, selecting the third directory down the list and pressing results
in moving down into the directory /home/hickey/ Ex4Man/.AppleDouble. It is possible to move up to the directory /home/hickey by selecting the ".." directory. As a final comment, Directories and Files can be double-clicked, thereby eliminating the necessity to press the Filter or OK buttons, respectively. Note that a Warning dialog (Section 2.13) will be activated if an inappropriate action such as highlighting Directory and clicking OK instead of Filter is performed.
The simulation output window may be printed by selecting Print selection from the File pull-down menu on the SEDPAK EXEC menu. This menu item has two options: to File and to Printer. Selecting File causes a file selection to appear. A Postscript file will be written to disk with the name specified in the file selection dialog. Selecting to Printer sends the output directly to the printer. Selection of the appropriate printer is location dependent. Therefore, the local installation's print command must be executed. The print command is specified in the .sedpakrc file which resides in the home directory of each user. (Setting up the sedpakrc file may require consultation with the local system manager). A print of the output may be obtained at any time by pausing the simulation run at the desired time and then selecting to Printer from the Print selection menu item.
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2.07 Sedpak Files
Two files which may assist in determining the status of SEDPAK execution. File names consist of a prefix, which is the name of the file being executed, and a suffix which is either .db or .log. The directory into which the files are written can be specified using the Option Command, discussed in the next section Section 2.08.
The database file (.db)
The data executed by SEDPAK are contained in the SEDPAK database file; all such files have a suffix of .db. The format of the file is described in the Technical Supplement to this manual.
The log file (.log)
The log file describes the data as it is used by the program. It includes the data that is accessed via the SEDPAK EDIT menu. It is because of the manner in which these data are represented internally by SEDPAK, however, that some additional interpolation occurs to the data entered to the program. For example, subsidence is defined by sets of depth-rate pairs at various locations but not all pairs are provided for every location across the basin and for every time. Thus, the program interpolates the values provided via the SEDPAK EDIT menu in order to have all the values needed by the simulation. These values are shown in the log file. Evidence of aliasing may also be seen in the log file. For example, sea level must be calculated for each time step of the simulation. If the number of time steps is small, then there may be two (time, depth) pairs which define sea level for the same time step. SEDPAK notes this in the log file.
SEDPAK also logs the amount of sediment deposited at each time step in this
file. In addition, SEDPAK logs the errors encountered during the simulation
and writes them to this file. This can be useful when trying to understand
problems related to errors which occur when entering the data for a simulation
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2.08 The Option Menu Command
The Option menu command, from the SEDPAK EXEC or SEDPAK EDIT menus, invokes the Initialization File Interface dialog (Figure 2.08.1) that is used to determine: whether the Balloon Help is to be "on" or "off", and, if "on", the time delay after the mouse pointer has come to rest over a menu button and before the Balloon Help is to be activated; the directory in which data files are located; the directory where .log files are written (refer to Section 2.07); and the specific commands to access a printer. If the location of the files or the print command needed to be changed, this can be done by typing in the appropriate field. For a discussion of the organization of these files and directories, refer to release notes provided with the SEDPAK distribution files.
Figure 2.08.1. Initialization File Interface dialog.
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2.09 The Balloon Help and Help Menu.
Help can be acquired in several ways. For instance if the mouse pointer is positioned over menu buttons on menu panels for a prescribed time, a short message is activated enclosed in a balloon and describing the action of that menu item. The time of onset of the Balloon Help following the positioning of the mouse arrow over a menu item can be set on the initialization file interface (Section 2.07, Figure 2.7.1)
Alternatively, Help can be obtained by selecting the Help icon on the SEDPAK LAUNCH menu or from the pull down menus on the SEDPAK EDIT, SEDPAK FACIES, and SEDPAK EXEC menu bars. Access to Help on the SEDPAK LAUNCH menu is handled differently from Help in the SEDPAK EDIT, SEDPAK FACIES, and the SEDPAK EXEC menus. The Help on the SEDPAK LAUNCH menu brings up the table of contents for the Help system (Figure 2.9.1) which acts as the starting point from which to acquire information on how to run SEDPAK. The SEDPAK LAUNCH Help system is organized in a manner similar to the printed SEDPAK manual. The viewer used for the Online Help system on the EXEC, EDIT, and FACIES menus is a Mosaic interface, from the National Center for Supercomputing Applications.
The Help system links can be accessed for further information by clicking on the words or pictures highlighted in blue. The first window displays a page which allows the user to browse through the online version of the manual, as though it were separated into sections and chapters. If the section for which Help is required is not visible, the list can be scrolled. Information for any section is selected by choosing the appropriate blue text in the list and clicking on it. The Forward and Back buttons can be used to move back to the previously accessed Help windows or forward to windows which had been selected earlier. The scroll bar on the right is used to view more text for the selected section. Some sections are accompanied by figures which can sometimes be viewed separately by selecting the appropriate figure numbers in the text. The Help window may be dismissed by pulling down the File menu at the top of the window and selecting Close Window or by selecting the close window button at the bottom of the Help window.
The pulldown menus under Help on the SEDPAK EDIT, SEDPAK FACIES, and SEDPAK EXEC menus provide access to Help on all the items listed on the SEDPAK EDIT, SEDPAK FACIES, and SEDPAK EXEC menus. The Help pull down menus list the following :
Table of Contents This provides help for SEDPAK Basics, SEDPAK LAUNCH menu, SEDPAK EDIT menu, SEDPAK EXEC menu, SEDPAK FACIES menu, Overlay, Adobe, Release notes, Technical supplement, and an Index. For further information, click on the words or pictures highlighted in blue.
Copyright Notice SEDPAK is a copyrighted software package. Further information about the copyright and licensing agreements can be found in this section of Help.
Help on Context
This powerful option activates the "Context Sensitive Help System" built into SEDPAK. When this menu item is selected, the cursor becomes a "?" which can be clicked on any menu item displayed on the SEDPAK menu interface from which Help was activated. The Help System will display information about that part of the interface.
Pictures and other information about the authors of the program.
Displays the first page of the Help system.
Figure 2.9.1. SEDPAK Help window.
Chapter 2, Section 10
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