Start here to learn key concepts, terms, conventions, and options for using Ecce.
|See also...||How to Acknowledge and Cite Ecce|
An Ecce calculation refers to
To run Ecce calculations, you must have UNIX accounts set up for 1) at least one machine where you can run the Ecce software, and 2) at least one Ecce-registered machine where the calculations can be processed and the appropriate computational codes are available. These may be the same machine. If you have accounts on several Ecce-registered machines, then you have more options about where to run calculations.
After your account(s) are properly set up, you can prepare and launch a calculation from your desktop workstation. Launch means to submit a calculation for processing on an Ecce-registered machine. Your desktop machine either runs the Ecce software or is logged in to a machine that can. The machine that runs the Ecce software is the launch machine. The machine that runs the computational codes is the run machine, sometimes referred to as the remote machine (even if it isn't really remote).
The inputs and results of calculations are stored on an Ecce Web server. This "database" of calculations is organized as a hierarchy of projects and calculations, roughly comparable to the folders and files of a personal computer. A project is a container that may include calculations and other projects. In this context, each calculation is an object that includes code input files, machine configurations, output files, and Ecce run logs. The Ecce Calculation Manager visually represents the calculation database as a collection of project folders that contain calculations.
Most Ecce users store their calculations in the "users" folder of the Web server, although it is possible to store calculations (and other Ecce objects such as chemical system structures) in any folder where you have read/write access.
/ users / username / project / calculation
A calculation also produces temporary files on the run machine--the Ecce-registered machine that processes a calculation. These include output files in a calculation directory and working files in a scratch directory. After successful completion of a calculation, the output files are copied from the calculation directory on the run machine to the project folder on the Ecce Web server, where they are stored as part of the calculation object.
|Note: These run machine files are NOT automatically deleted: they can be useful for diagnosing run problems and for backup in case of network failures. You can (and should) clean up these run directories periodically to conserve disk space. See the Calculation Manager's option for Run Mgmt: Cleanup Run Directory Files.|
Calculation property data displays are dynamic. Most displays of Ecce data are updated to reflect the changing conditions (as a running calculation completes each processing step, for example).
It will be helpful to understand the following conventions as you interact with Ecce tools and processes.
You can start the major Ecce tools either from the Gateway or from the Tools menu of an Ecce tool window. Although many tools operate in the context of a single calculation, you can open multiple instances of a tool window to work on more than one calculation at a time by shift-clicking on a tool icon in the Gateway or on a menu item in a Tools menu..
|How to...||Manage Tools on the Desktop|
Most major tool windows include a menu bar for choosing task options and a window footer.
|Tip: Open any menu from the keyboard by using the Alt+underlined letter combination (for example, Alt+h opens the Help menu). Then select a menu option by pressing the letter that corresponds to the option.|
|More about...||Items in the Ecce Window Footer|
The labels on buttons and in menus convey the following information by their appearance.
||Dark labels - indicate that the option is available.|
||Grayed-out labels - indicate the option is not available in the current context. The option will become available under other conditions.|
|Ellipsis marks (. . .) - indicate that the option will open a separate window or dialog for further interactions.|
The mouse cursor and various elements of Ecce tool windows provide visual feedback about current operations and conditions.
|Mouse Cursors||The mouse cursor will change color and shape to indicate the status of various operations. For example:|
|Yellow cursor - indicates Ecce is processing a request (such as opening a tool after you click on an icon in the Gateway).|
|Stopwatch cursor - indicates Ecce is processing a tool request (such as loading calculation properties into the Calculation Viewer after a drag-and-drop from the Calculation Manager).|
||Drag & Drop cursor - indicates that an information object is being dragged. The cursor turns green when it points to a drop site where the object can be dropped. The cursor turns red when it points to a drop site where the information is inappropriate and cannot be dropped. The actual appearance of the drag & drop cursor varies, depending on the graphic interface of your system.|
|Hand cursors - indicate various types of chemical system manipulation operations in the Builder tool.|
|Icons||Special icons in the Gateway or in tool windows indicate the status of programs or data.|
|Ecce wave animation (System Busy icon in the Gateway) - indicates
that an Ecce tool is opening.
|Calculation state icons - indicate (by their shape and color) the preparation or processing state of Ecce calculations. For more details, see Legend of Calculation Run States in the Calculation Manager.|
|"Save Work" star icon - indicates that your work in an Ecce tool has not been saved to a database. (Click on the star icon to save your work and remove the Save Work icon.)|
|Padlock icon - indicates that you cannot change inputs in the current window at the current time, such as the inputs of a running calculation.|
Ecce's drag & drop operations enable you to use the mouse to move several kinds of information within and between Ecce tools. By use of the middle mouse button, certain information objects can be quickly dragged from one location and dropped at another. Examples:
The information actually transferred between tools depends on what information is usable in the destination tool. For example, a calculation object dragged from the Calculation Manager can load the Builder with the calculation's chemical system or load the Calculation Editor with the calculation's current input parameters.
|How to...||Drag & Drop with the Mouse|
|Move a Project or Calculation in the Calculation Manager|
Drop Sites. Information can be dragged only to a drop site - a destination for "drag & drop" operations.
|Warning: Dropping on a drop site that is not ready (usually because it is still processing the last drop) may cause crashes. See how to Drag & Drop with the Mouse (above).|
|The square "in-tray" area in the lower right corner of many Ecce windows is the main type of drop site for receiving information from other tools.|
|In the Calculation Manager's project tree, you can move or copy (Ctrl + ) one of your project folders by dragging and dropping it onto another of your project folders.|
|Summary Caption||In the Calculation Viewer, summary item captions can be rearranged by dragging and dropping them onto each other.|
|Exportable Data||Export Format(s)||Tools and Options|
|Chemical system||molecular structure and graphic formats||Builder
/ File menu / Export
|Structure Library / Structure menu / Export|
|graphic formats||Calculation Viewer / Calculation menu / Export|
|Values for a calculated property (table)||spreadsheet-readable formats||Calculation Viewer / data panel / pop-up menu / Export|
|Basis sets selected for a chemical system||ASCII file||Basis Set Tool / Molecular Basis menu / Save to File|
A general printing option in several tools enables printing either to a postscript file or to a postscript printer selected from a list of available printers.
|Printable Data||Tools and Options|
|Chemical system image||Builder / File menu / Print|
|Calculation Viewer / Calculation menu / Print|
|Values for a calculated property (tables and graphs)||Calculation Viewer / data panel / pop-up menu / Print|
Importing options include molecular structures and completed calculations.
|Importable Data||Import Format(s)||Tools and Options|
|Chemical system||molecular structure formats||Builder / File menu / Import|
|Structure Library / Structure menu / Import|
|Basis Set Tool / Browse Options menu / Import Fragment|
|Calculation (code outputs)||
NWChem output file (ecce.out)
|Calculation Manager / Calculation menu / Import|
Ecce includes several preferences that you can set to control the behavior and appearance of Ecce tools. Preferences include the date format, the colors associated with calculation run states, and some units (energy, distance, frequency).
If you need to run both Ecce v2.1 and v3.0 or higher back to back, Ecce offers a simple mechanism to support switching preference files between versions. When you first start v3.0, Ecce recognizes the presence of any v2.1 preference files and converts them to v3.0 format. The v2.1 files are copied to files of the same names with extensions of .v2.1. By copying the .v2.1 files back over top of the v3.0 counterparts, the older version of Ecce can be run again and Ecce will re-convert the files to v3.0 format when that version is run. A new script named reformat_machines is automatically called by Ecce to do this conversion for you.
|How to...||Set Preferences|
|Ecce Online Help
Revised: April 29, 2004