Introduction to Mac OS X The Mac OS X operating system both a graphical user interface and a command line interface. We will see how to use both to our advantage. Using DOCK The dock on Mac OS X is the Application bar which by default is situated at the bottom of your screen. It is similar to the Task Bar on Windows. The dock is customizable (see Mac help for more info). To launch applications in your Dock, click on their icon once. A black triangular shape appearing under the icon indicates that the application is currently open. Adding a shortcut for an application You can add easily an item to the Dock. For example we are going to use the software MacMolPlot along the sessions so let's add it into the Dock. First you need to open a Finder window and click on the Application short cut on the left of the window, like it is shown below:
When you reach the icon of your application (in our example MacMolPlot) you simply click and keep the button pressed until you drag the icon into Dock where you simply drop it. Now you can see the icon of MacMolPlot in your dock so by clicking on it you can open the application. Using FINDER Finder on mac OS X is the same as the "Windows Explorer" on Windows. Finder gives you lots of options to locate, display and organize all your files and folders. The 3 buttons we circled on the picture allow you to modify the display as you like to visualize your folders. From Finder you can open an application by double clicking on it. It works the same for the files. Each kind of files has an application assigned by default to open it, so when you double click on a file it will be open with that application.
You can also drag and drop the file on the icon of the application in Dock with which you want to open that file. Using X11-terminal On your mac you will find two kind of terminals. One installed by default which is called "Terminal" and one installed by the user called "X11". The X11 terminal is a X window. It allows the user to display graphical interface on Unix-like operating systems. X11 terminal is in the Utilities directory under the Applications. Launching X11 Usually when you install the developper's tools on your mac, X11 terminal is installed under the Utilities directories. As we plan to use X11 a lot, it would be useful to add it in the Dock. Then to launch the X11 terminal it will be easy to click on the icon in the Dock After clicking on the icon, it will begin activate and a little black triangular shape will appear under the icon to mention that the application is opened. And then a X11 terminal will open.. The X11 terminal is used as a Unix terminal as all of the standart UNIX utilities and scripting languages are included in Mac OS X: editors like emacs, vi (you will see later), file management tools, shell scripts... Hints on Mac OS Web Browser The most popular browser for mac users is now Safari. we will be using this browser in this course. If it is not in the Dock you can drag and drop the icon of Safari from the Applications folder.
Enable tabs on Safari First go to Safari menu and select Preferences. The Preferences window opened, you will click on the tabs icon on the top. Then activate the option called "Enable Tabbed Browsing". Activate the tabbed browsing on Safari. Shortcuts with Safari: Open a new tab: command + t Open a link in a new tab and select it: command + click Open a link in a new tab: command + shift + click Open a link in a new window and select it: command + option + click Open a link in a new window behind the current one: command + option + shift + click Access the search field: command + option + f Increase font of a webpage: command + Plus-sign Decrease font size of a web page: command + Minus-sign Quit an application properly When you want to quit an application you close the window by clicking on the red button. BUT the application is not quit, it is still opened. So to close the application you need to go to the menu of the application and select Quit, or simply use the short cut: command + q.
You can check if you let application opened by looking at the Dock. All applications open have a black triangular shape under the icon that disappears when you quit the application. Checking this avoids to have too many applications opened. Shortcuts on Mac OS: keyboard commands On Mac the keyboard is slightly different than on Windows machines. The most important difference is the Apple or command key. This key is used much like the Control key on a Windows machine. Also many shortcuts in programs on a Windows program will work with the Apple key on the Mac. Text Copy: command + c Paste: command + v Cut: command + x Undo: command + z Redo: command + y Select all: command + a Window Close window:command + w Close all windows: Option + command + w Menu Command Log out: shift + command + q Log out immediately: shift + option + command + q Hide the active application: command + h
Hide others application: option + command + h New windows: command + n New folder in Finder: shift + command + n Open a new document: command + o Save a document: command + s Save as: shift + command + s Print menu: command + p Move to Trash: command + delete Other Commands Switch application: command + tab Force quit: option + command + ESC Restart, Sleep, Shutdown dialog box: control + eject Sleep: option + command + eject(buton on the left-up corner) Quit all applications and restart: control + command + eject Reference to learn more shortcuts on Mac: http://support.apple.com/kb/ht1343 Introduction to Basic Unix commands The Graphical User Interface (GUI) of Mac OS X provides a visual "userfriendly" layer that provides visual cues to help users use their computer with greater ease. The same operation can also be done typing in a command on the "command line". For example, dragging and dropping a file HelloBaby.txt into folder PinkyToes could be done on the command line using: mv HelloBaby.txt PinkyToes To use the command line on a Mac you need to open a terminal In unix, tasks often use the following syntax:
Syntax of a Unix Command This example shows how to copy a directory called folder1, making a new directory called, folder2. Useful tip! Wildcards can be used to add flexibility to your commands: The most common wildcards * For example: ls *.inp returns the list of files with the extension ".inp" in the directory. Another common wildcard is:? For example: ls my??put.inp => return the list of files with 2 letters to replace the two?. Common Command lines Information: Any time you wish to find information about how to use a command properly, you can type: man the_command_of_interest This will open the unix manual for the command, which you may scroll through using the arrow keys, or by pressing the letter "f" for "forward" or the letter "b" for "backward", and you can exit the manual by pressing the letter "q". Try, for example, typing: man cd In your command line window, to see information about the first command listed below. Directory cd [directory] change directory mkdir directory_name make a directory rmdir delete an empty directory rm -r directory delete the directory
File ls [options] directory or file list directory contents or file permission pwd find out which directory you are in cp [options] file1 file2 copy file1 into file2 cp [options] file1 file2 copy file1 into file2 less [options] file page through a text file o o o [shift] g => go the end of the file [ctrl] d => go 10 lines down [ctrl] b => go 10 lines back tail -f filename Show the line at the same time as they are written tar [options] archive_name.tar files_name combined multiple files and folders into a single file, but does not compress anything. gzip [options] file_name > ar archive_name compress files gunzip [option] archive_name Extract the files from the archive bzip2 [option] filenames create a compressed file.bz2 bunzip2 [option] archive.bz2 Uncompress the compress file Find find directory -name file Look for a file in a directory and his content grep pattern file Look for a pattern in a file Processes ps -al display the processes jobs display the tasks ctrl z interrupt the current task ctrl c Stop the current task kill -9 processus_number kill the processes bg job_number put a task in background fg job_number put the task in front Right ls -l filename list file permissions chown [option] file modify the owner of a file/directory chgrp file modify the group
Introduction to VI There are many VI tutorials and cheat sheets on the web. VI Tutorial : http://www.cs.colostate.edu/helpdocs/vi.html List of VI Commands: http://www.unix-manuals.com/refs/vi-ref/vi-ref.htm Why bother learning VI? It is installed by default on UNIX systems. The key to learning VI is to keep in mind the 2 principal modes that are the text-insert mode used to add text to a file and the command-mode used to give commands. The ESC key has to be pressed to pass from one mode to another one. To invoke VI: vi filename If you did not already have the file, this command will create it. VI modes Editing mode Edit mode allows you to move the cursor and edit the text buffer. It is the default mode when you open a file with vi. Inserting mode Insert mode "drops" the cursor at a specific point in the buffer, allowing you to insert text. i Insert before cursor. I Insert at start of current line. a Append after cursor. A Append at end of current line. o Open new line below. O Open new line above. Command mode Command mode moves the cursor to the command line, allowing you to invoke program commands such as write to file (:w) and quit (:q). You enter colon mode from edit mode by typing a colon followed by a command. :w Write buffer to the current filename.
:w newname Write buffer to file newname. :r Read the current filename into the buffer. :r oldname Read the file oldname into the buffer. :q! Quit vi without saving buffer. :wq Write buffer to current filename and quit vi. :e filename Close current buffer and edit (open) filename. :e # Close current buffer and edit (open) previous file. Cursor movement In addition to the arrow keys, you can use these edit mode commands to move the cursor: h Left one character. j Down one line. k Up one line. l Right one character. b Beginning of previous word. e End of next word. w Beginning of next word. { Backward one paragraph. } Forward one paragraph. ^ Go to first character of current line. $ Go to last character of current line. CTRL/d Forward (down) one-half page. CTRL/u Backward (up) one-half page. CTRL/f Forward one page.ctrl/b Backward one page. G Go to the end of the file. 1G Go to the first line of the file. ng Go to line number n. Searching in VI editor / The slash is the symbol to indicate you wish to search for whatever follows (make note that this is case-sensitive) E.g.) /GAMESS will result in a search for the word GAMESS in your file, an bring you to the next location ahead in the file containing the word
Typing / again will result in proceeding again foreward in the file to find the next location of the word GAMESS.? The question mark is also a search symbol, to search backwards from your current position in the file. E.g.)?ENERGY will search backwards for the word ENERGY previously written in the file.