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There is also the issue, raised by Tom Christiansen in a Usenet article in 1992 (viewable here), that GUIs make simple things simple and complex ones impossible. A program designed to work solely from the GUI isolates the program from all others. Scripts can not be written to control graphical applications and combine them with other programs to solve a larger more complex problem. Graphical programs are also difficult to run remotely -- something we find ourselves doing more often now that large parallel processing machines are used for flow solutions.
Lastly, graphical programs tend to slow down experienced users. Even a moderate typist can enter commands faster from the keyboard than from a GUI -- and usually with less error.
Like all of engineering, the answer lies in a balance. CFD applications should first and foremost be command-driven "batch" programs able to be controlled through simple keyboard actions (or scripts). Only then should a well-designed graphical interface (one which makes liberal use of keyboard shortcuts) be placed on top of the application.
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