ARE YOU STILL SERIOUS ABOUT CERIUS?


INDEX



FOREWORD

CERIUS is installed in VisLab on LEWIS (UNIX workstation): you will need to book time on LEWIS as this workstation can sometimes get very popular among users.

Access to VisLab is limited : you will need to get before hand a computer account and a card to get inside (inside VisLab, not the computer!).

VisLab: (61) 2-351 3005 (Contacts: Prof. B. Pailthorpe, Ben Simons )

A minimum knowledge of UNIX is required to run CERIUS. Section XVI is for those UNIX illiterates!

The following are general guidelines to get started with CERIUS and the following modules: MODELS , CRYSTALS , HRTEM , CONTROLS , GRAPHS . It is really intended for people who make a cold start on CERIUS and do not want to wander (and wonder!) in the Serious manual.

Remember that at any time within CERIUS, you can get on-line help by clicking with the right mouse button on the item for which you want help and of course, if everything else fails, you still can read the manual!

You are welcome to make any comments and suggestions regarding these notes to Nicole ( nicole@vislab.usyd.edu.au).


I- OPTIMUM CONFIGURATION TO RUN CERIUS


  1. because files created by CERIUS can use a lot of disk space, it is advisable to be nice to the system manager and ask Ben to create a scratch space from where you will run CERIUS.
  2. bring a sweater: it can get cold in FreezeLab sorry! VisLab.

Warning :
The scratch space is a temporary disk space: files kept there will eventually be erased without mercy so copy anything important back to your home directory!

NB: If you are a fan or a user of the EMU's Philips 430, get the EM430.mic file from Stephen, Chou or Nicole: all relevant 430 parameters are in it.


II- GETTING INTO CERIUS


Fig. 1 ):

Troubleshooting :
  1. nothing happens on the screen and you get error messages:
    • type ls -al on one of the UNIX shell
    • remove the core file by typing rm core (it usually does wonders! Don't know why though!).
  2. nothing happens on the screen but you do not get error messages:
    • the CERIUS model window might have been minimized during a previous session: click on it to display it on the screen.
  3. no text window:
    • check you have a console window somewhere on your screen: the titlebar of the console window should read myname@lewis create a console by selecting Start New Console System Desk 1 run CERIUS once more.
Tip :
create an alias to get to the scratch directory directly (eg.: in your .chsrc file or .alias file, enter alias scratch 'cd /scratch/username' ).

II-b Deck of Cards

  1. switch between the decks by clicking on the arrows below Menu Deck ( Fig. 2 ).

  2. select a module by clicking on its name: the module will be displayed at the front of the deck.
Tip :
it is a good idea to have all the modules that you will use, displayed on Deck A: select Edit in the Deck Menu window; move around between the decks to place the menus that you want on deck A. When happy, select Save . The next time you run CERIUS, the program will automatically load these settings.

II-c Non Essential General Info that you should Know

  1. bright pink buttons brings up menus (button's name is followed by >).
  2. dark pink buttons brings up windows or perform an action.
  3. to type something in a box, the cursor must be inside the box.
  4. on-line help is available by clicking with the right mouse button on the box you want some info on.
  5. an option selected is displayed with a tick or a cross in the box.
  6. exit from a window by clicking on .... Exit !
  7. if you eyesight is no longer what it used to be, CERIUS windows can be resized, moved, etc, with the usual UNIX controls (no pull-down menu on some windows):


III- VIEWING CONTROLS


  1. in the Atom Display Manager window ( Fig. 3 ), select the style (it is Stick by default): you have the choice between six options (stick, ball, cylinder, ball/stick, poly, ellipsoid).

  2. click on Styles... to select the size and resolution corresponding to the style you just chose.
Tip :
if the model is big, keep the size and resolution of the atoms small.

To load an existing model, go to IV ; to create a model, go to VI but read V .


IV- LOADING AN EXISTING MODEL


Tip :
CERIUS automatically calculates and displays the bonds between atoms when loading a model. To speed up things, before loading the model, select the Crystals card in Deck A (see Fig. 6 ), then Crystal Building and click on Auto-Bond Calculation (the tick mark disappears). You can have CERIUS recalculate the bonds later.

IV-a Loading a Model

  1. load a model by selecting the Models card in Deck A (the card is displayed in front of the others):
NB 1 : more than one model can be displayed but the commands will only affect the active model.

NB 2 : CERIUS can not load several very large models (>10000 atoms) at the same time: you will have to do some clearing!

NB 3 : CERIUS can accept 11 file formats. Among them, cssr file (Cambridge Structure Search and Retrieval) is the format recommended for use as a standard with CERIUS and is the default setting.

IV-b Clearing a Model

  1. click in the box located at the left side (current column) of the model's name that you want to make active.
  2. to clear a model, make it active and select the Models card:


V- MODEL MANAGER


  1. to display several models, choose Multiple Display Style Border in the Model Manager window.
  2. click on box at the right side of the model's name (column additional): any additional model will be displayed on the border (see Fig. 10 ).
  3. options other than Border are available, such as Overlay and Grid.


VI- VIEWING A MODEL


These controls will only affect the way you see the model, not the model itself.

Tip :
if the model is big, manipulating the view can be very slow: changing the style to Ellipsoid for instance, using the lowest resolution and size (Styles...) will help ( View Manager window).

VI-a Dials

  1. click on Dials of the View Manager window ( Fig. 5 ):

NB : Using the dials is less accurate than typing a number

VI-b Mouse and Function Key Controls

The cursor must be in the model window:
  1. right mouse button: rotation about axis in xy plane (the axes lie in the plane of the screen).
  2. shift and right mouse button: rotation about z-axis (in the plane of the screen).
  3. control and right mouse button: zoom in and out.
  4. middle mouse button: translation in the zy plane .
  5. left button click on atom: atom selection .
  6. shift and left button click on atom: obtain information about atom.
  7. F1 : toggle into/out of full screen.
NB : If you have made a mess or you do not know what you are looking at, you can reset the view by clicking in the View Manager window the appropriate box: View, Pan, Zoom or All.

VI-c Selecting-Deselecting Atoms

  1. to select an atom, click on it with the left mouse button; to deselect it, click on it again. Simple, isn't it!
  2. to select all atoms, click on Select All in the Selection Manager ; to deselect all atoms, double click in the Selection Manager an empty space of the Model Window or click on Deselect All in the Selection Manager .
  3. to select a group of atoms in an area of the screen, click and drag the resulting yellow box with the left mouse button around this area: all atoms within the box will be selected.


VII- CREATING A MODEL


  1. select Crystal Building from the Crystals card in Deck A ( Fig. 6 ).
NB : the atoms can be fitted into the unit cell by default , in-cell , molecular or original .

VII-a Crystals

  1. Creating a crystal: the unit cell can be created from the space group or from scratch .

a) Creating a unit cell from a space group:

  1. select Space Group and enter the space group name (international notation) and type a blank between each letter.
  2. select Edit Cell Parameters ( Fig. 7 ):

  3. select Add Atoms... ( Fig. 8 ):

  4. select Build Type in-cell .
  5. select Auto-Bond Calculations , if you want to have the crystal bonding calculated.
  6. select Build Crystal .
NB : at any time, you can undo your crystal by selecting Unbuild Crystal .

b) Creating a unit cell from scratch:

  1. select Edit Cell Parameters ( Fig. 7 ): NB : At any time, you can undo your crystal by selecting Unbuild Crystal .

  2. Assembling several unit cells:
  3. from there, one can create a superstructure (non repeating structure) or a superlattice (repeating structure):

    a) Creating a superlattice:
    1. click on Superlattice : the new structure is displayed, you can not undo it.

    b) Creating a superstructure (non repeating structure):
    1. click on Superstructure : the new structure is displayed, you can not undo it.

Tip :
it is a good idea to save your model before creating a superstructure or superlattice. See VIII on how to save a model.

VII-b Polycrystals

  1. Creating a polycrystal:
    One can think of a polycrystal as a big number of little crystals (crystallite) randomly arranged in a volume: create several superstructures as described in VII-a of different sizes (for example: one 2x2x2, one 3x3x3 and one 4x4x4).
    1. load each crystallite so they appear in the model manager.
    2. select Border display.
    3. click in the box located at the right side ( additional column) of the models' name you are going to use: the active model is displayed in the center and the other models on the border.
    4. click and drag from the crystallite to the model display as many times as necessary ( Fig. 10 ).

    5. select one crystallite: while holding the left mouse, click and drag the mouse over the crystallite (the atoms inside the yellow rectangle are selected):
      • select the Models card.
      • to translate the crystallite, select Geometry and Translate : select the direction of translation and type the amount of translation inside the boxes.
      • to rotate the crystallite, select Geometry and Rotate : select the direction of rotation and type the amount of rotation inside the boxes or use the dials (less accurate).
      • rotate and translate the remaining crystallites.
      • when happy, select the Crystals card.
      • select Crystal Building and Crystal Parameters : enter the size of the polycrystal.
      • select Build Type Default .
      • select Build Crystal (for big models, this might take 3 or 4 minutes).

    NB : Models within CERIUS are limited to 14000 atoms. For some reason, some users have had problems to save models with more than 10000 atoms.

  2. Making a different polycrystal from the previous one:
    If all atoms within the polycrystal are rotated, you get a "new" polycrystal.
    1. load the polycrystal in the model manager.
    2. click on Select All in the Selection Manager window.
    3. select the Models card then Geometry and Rotate : select the axis of rotation and type the amount of rotation inside the boxes.
    4. click on Deselect All in the Selection Manager window.
    5. some atoms are outside the polycrystal's "unit cell": select those atoms to be trimmed.
    6. select Edit in the Models card then Edit Atoms ( Fig. 11 ).

    7. set to edit selected atoms (it is single by default)
    8. click Delete Atoms .

NB: Another way to do a polycrystal is to create several " 2-D layers " of random crystallites using the method described on VII-b and superimposing these layers ( Fig. 12 ).

VII-c Something Cool and Fun!

Since you have come so far, you deserve a little reward!
  1. ask one of the guys in VisLab if you can use the stereo glasses.
  2. from the Models card, select View and then Preferences .
  3. set Display projection to Perspect , stereo viewing style to Crystaleyes .
  4. turn the infrared emitter on.
  5. put on the stereo glasses, turn them on and click on Stereo .
  6. F2 toggles into/out of stereo mode.
  7. control and left mouse button provides control over the stereo separation.


VIII- SAVING A MODEL


  1. select File from the Models card, then Save .
  2. choose your directory.
  3. give a name to the model without the extension (cssr extension is selected by default)
  4. click Save : you will get a beep and an acknowledgment in the text port.
Tip :
It will never be said enough: save your models frequently !


CONGRATULATIONS! YOU CAN DO SOME SERIOUS SIMULATIONS AT LAST!


IX- HRTEM


NB : Multislices calculations can only be done along the following axes (001), (010) and (100). For an other crystallographic direction, you need to play around with the model so that the crystallographic direction you are interested in is parallel to the CERIUS (001) axes. If you are satisfied with one slice, you can use any orientation you like!

IX-a Microscope Parameters

  1. select the HRTEM card .
  2. select Microscope Parameters from the HRTEM card ( Fig. 13 ).

  3. enter the characteristic parameters of the microscope or load the EM430.mic file which has the parameters of our beloved 430, or enter your own microscope's parameters (.mic file).

IX-b Create Slices.

  1. select Create Slices from the HRTEM card ( Fig. 14 )

  2. choose the Zone Axis : CERIUS selects two reciprocal lattice vectors a* and b* which are perpendicular to the zone axis.
  3. click on Initialise Scattering Geometry .
  4. choose the number of beams (a* and b*) and CERIUS calculates the maximum wave vector (Max k) or choose Max k and CERIUS calculates the number of beams (maximum is 512x512).
  5. select Preferences :
  6. check you have the right beam energy (most people use 200 or 300 kV machines).
  7. select Preferences (ptf part of the window, next to electron energy): enter a value for the absorption coefficient ( 0 by default).
  8. you can change the seed file name (if you don't like hrm) and the seed number.
  9. click on Create Projected Potential File .
  10. the first files created are hrm001.ptf and hrm001.prj : it is created by adding the seed number to the seed file; the seed number increments by one after each slice calculations. You can check the progress of the calculation on the text port.
  11. have a cuppa: this part of the calculation can take up to 30 minutes for large models!

IX-c Crystal Propagation.

  1. select Crystal Propagation from the HRTEM card ( Fig. 15 ).

  2. enter the seed file name if different from hrm.
  3. type in the slice numbers in the reverse order (from the highest to the lowest number); for instance: 4 3 2 1 or 4-1; the ptf files are listed from last slice to first.
  4. choose the maximum wave vector ( k Max ) and CERIUS calculates automatically the number of beams a* and b* or enter the a* and b* save range and CERIUS automatically calculates k Max.
  5. select the frequency with which the diffraction files (hrm001.dif) are saved.
  6. click on Start Propagation .
  7. hrmxxx.dif files are generated.

NB : In the text port, the first column of big numbers represents the intensities in the through beam, the second column the intensities in the central two-thirds of the scattered beam and the third column the intensities of the outer-most beams.

Tip #1:
in the case of a crystalline model ( periodic ), you can increase the size of the crystal in the direction of the propagation by typing i(n-m) where n is the nth slice, m the mth slice and i an integer (for instance, n(4-1) for 4 slices). The crystal will appear to have a i*height in the propagation direction.

Tip #2:
in the text port, monitor the last column which represents the intensities of the outer-most beams: it must not become greater by 1% .

IX-d Microscope Propagation.

  1. select Microscope Propagation from the HRTEM card ( Fig. 16 ).

  2. double click on the .dif file inside the file browser.
  3. if you want to save a picture of the calculation, tick in the box (default name is hrmxxx.pic).
  4. CERIUS gives you the possibility to do a Defocus series: enter the number of steps and the range of the defocus.
  5. click on Propagate .
  6. hrmxxx.pic files are generated.
  7. the defocus series will be displayed in the Graph window.
NB 1 : Only the last picture of the defocus series is saved and can be printed. A reward will be offered to whoever can manage to have all the defocus series pictures printed in one go!

NB 2 : It is better to save the pictures as graph files ( .grf ) rather than as HRTEM pictures (.pic): the format is much easier to manipulate for other programs and the viewing conditions are saved too. See IX-e 2,3 on how to save pictures in .grf format.

IX-e Displaying and Saving Graph.

  1. select Display from the HRTEM card ( Fig. 17 ).

  2. double click on the file you are interested in inside the file browser: or type the name of the file you want to see into the appropriate box (prj, ptf, dif, pic)and click on the Plot button. The picture is displayed in the Graph window.
  3. select File from the Graphs card and Save (grf format by default); you will get a beep and an acknowledgment in the text port.
  4. you can now improve the display:
NB : If you checked in the Create Slice card Automatically Delete prj files , you will not be able to look at those files.

Tip :
go on a log conversion for diffraction patterns and play with the intensity values (decreasing the highest intensity value works fine).


X- PRINTING


  1. select Hard Copy from the Controls card ( Fig. 19 ).

X-a Printing a Graph.

  1. check that you are capturing a graph ( Graph is displayed) and colour type is set to black/white (diffraction pattern) or greyscale (image).
  2. click on Save : the image is saved under the name out.ps if you do not specify another name.
  3. click on Print .

X-b Printing a Model.

  1. select Model .
  2. change the background from black to white .
  3. CERIUS captures the model window so make sure that no other window is overlapping.
  4. click on Save : the image is saved under the name out.ps if you do not specify another name.
  5. click on Print .
  6. revert the background to black .

X-c Printing several graphs on one page.

  1. select Gallery then Manager from the Graph card.
  2. tick on the files you want to have printed.
  3. select Hard Copy from the Controls card.
  4. click on Save : the image is saved under the name out.ps if you do not specify another name.
  5. click on Print .
NB : It takes about 5 minutes to print a graph and 15 minutes to print a model.

Tip :
If you are printing several pictures in a row, do not use the default name (out.ps) but give a different name each time.


XI- INTERRUPTING CERIUS


A laugh does not interrupt Serious.

There are several ways to interrupt CERIUS like pulling out the plug from the wall but for your safety or if you value your life, it is recommended to stick to the following:

  1. click on Interrupt (above the Model Manager) or
  2. place the pointer in the text window and type Ctrl-C .
  3. a dialog box will pop up within seconds asking you about your real intentions.


XII- EXITING CERIUS (VOLUNTARILY)


  1. select File and Exit CERIUS from the Models card.
  2. move all the files you want to keep to your home directory.
  3. remove unnecessary files.


XIII- MORE SERIOUS STUFF


XIII-a Miller Planes.

Miller planes can be displayed when building a crystal:
  1. select from the Crystals module, Crystal Building then Visualisation Options .
  2. enter the h,k,l values and click Enter .
  3. tick on the option Show Miller Indices .

XIII-b Changing an Element Parameters.

to change the radius of an element, its color, ...
  1. select from the Models module, Define Element Attributes .
  2. do your changes.

NB : Some colors do not transfer very well on the laser printer (or other media), have a test before trying to print a big model.

XIII-c Replacing an Element by Another Within a Structure.

  1. select from the Models module, Edit then Edit Disorder .
  2. enter the name of the elements you want to change and add.
  3. enter the ratio
  4. click on Substitute .

XIII-d Bonds (bonds have more fun!).

You can change the bonding between all atoms or the atoms of your choice.
  1. select from the Models module, Edit then Edit Bonding ( Fig. 20 ).

  2. select the atoms in your model that you want to bond and select Selected (default setting) or select All if you want to recalculate the bonding between all atoms.
  3. click on Bonding Criteria to set your criteria (this window can be accessed independently by selecting from the Models module, Define then Bonding Criteria ).
  4. when ready, click on Recalculate Bonding .
  5. if you want to remove the bonding, click on Remove Bonding .


XIV- DATA STORAGE


If you take too much space on the disk, you might become impopular!

There are two ways to store your data: locally in Sydney on a DAT tape that you can purchase from Ben (it will cost you about $15) or remotely on a tape in a special place in Canberra. The advantages in using Canberra are that you do not need to get a DAT tape, space is not a problem, the transfer is faster and frankly, it is easier! The only disadvantage is that the transfer is subject to the connection between Canberra and Sydney (and potential political problems between the two cities).

Tip :
Have everything you want to store/back-up ready in a directory. Do the transfer and check that everything went well before deleting your files.

XIV-a National Tape Robot.

This service is a semi-infinite tape archive at ANU (Australian National University for the tourists) and is only available from Stacey .

NB : If you do not have an account in the Canberra "space", have one of the guys in VisLab created one (it takes two minutes).

  1. connect yourself to Stacey; you can either:
  2. type cp * /nfs/archive/myname (you should now know what that means!).
  3. type cd /nfs/archive/myname : this gives you the prompt /nfs/archive/myname; within this directory, you can create/remove directories and files.
  4. type l and check that the transfer went well.
  5. cd takes you back to Sydney, in your home directory.

XIV-b DAT Tapes.

If you do not trust Telecom or if you like difficulties, you can copy your files on a DAT tape yourself (may be not the first time!). The tape drive is located on Mudford and connected to it. The tape drive store data sequentially in blocks which are referenced by their position on the tape.
  1. put a tape in the drive (it works better!): if you have a blank tape, go to 4.
  2. type mt -t mudford:/dev/tape status to see where you are on the tape (just in case you did not rewind the tape the last time and do not know where you are).
  3. type mt -t mudford:/dev/nrtape feom to fast forward to the end of media..
  4. type tar cvf mudford:/dev/nrtape filename (or directory ): this creates a block and copies the file or directory into it.
  5. type mt -t mudford:/dev/nrtape bsf n to go back n files.
  6. type tar tvf mudford:/dev/nrtape to see what is in the current block.
  7. type mt -t mudford:/dev/tape rewind to rewind the tape.
  8. type mt -t mudford:/dev/tape unload to eject the tape.
  9. type tar xvf mudford:/dev/nrtape to extract the current block.
  10. don't forget your tape!


XV- TUTORIAL: SILICON ON A SILICON GRAPHICS MACHINE.


Silicon (Si for the friends) belongs to the Fd3m space group ( diamond structure) and has a lattice parameter of 5.4306 Å .

We will hopefully get a high resolution picture of a crystal of silicon as well as a diffraction pattern in the (001) direction.

XV-a Meeting Serious.

  1. locate Lewis in VisLab.
  2. enter your username and password .
  3. check you have a console window: the titlebar of the console window should read yourname@lewis . If you do not have anything like that, go to Desk 1 and select Start New Console under the System menu.
  4. create a shell (select Shell under the Tools menu in Desk 1 ).
  5. if you have a scratch space, type cd /scratch/yourname ; if you do not have a scratch space, that is all right for now.
  6. type cerius in the shell: it will take a few seconds.
  7. in the Atom Display Manager , change the style to Ball .
  8. click on Styles... in the Atom Display Manager and adjust the size and resolution to a lesser value than what is set.

XV-b Building a silicon crystal.

  1. select Crystal Building from the Crystals card.
  2. select Build Type in-cell if it is not already ticked.
  3. tick in Auto-Bond Calculations : we want to have the crystal bonding calculated.
  4. select Space Group and enter F d 3 m (insert a blank space between each letter): CERIUS displays F d-3m and you can see in the Space Group Information window that the lattice type is indeed cubic and face-centred (centered for those who speak american).
  5. select Edit Cell Parameters and enter 5.4306 : CERIUS is clever enough to set b and c to this value. Click on Exit .
  6. select Add Atoms...
  7. select Build Crystal : you should get something that looks like Fig. 21 ; if you don't, you have created something else!

  8. save your Si unit cell (select File from the Models card, then Save ).
  9. select Visualization Options : enter for instance 5 5 5 and click Enter : the crystal is 5 unit cells long in the a, b, c directions; click on Exit .
  10. click on Superlattice .
  11. click on Exit on the Crystal Building card.
  12. save your Si structure (select File from the Models card , then Save ).

XV-c Slicing Silicon...

  1. select Create Slices from the HRTEM card.
  2. enter 1 0 0 in the Zone Axis box: CERIUS selects two reciprocal lattice vectors a* and b* which are perpendicular to this zone axis.
  3. click on Initialise Scattering Geometry : on the text port the folowing is displayed:
  4. leave the number of beams a* and b* to 160 : Max k= 2.95 Å-1 .
  5. select Preferences :
  6. enter 300 for the beam energy (EMU influence); we will not enter a value for the absorption coefficient.
  7. click on Create Projected Potential Files : CERIUS is doing the calculations; since it is a very small calculation, it only takes a few minutes: sorry! no time for a cuppa!
  8. you should have 10 files named hrm00n.ptf with n varying from 1 to 10 .

XV-d Crystal Propagation.

  1. close the Create Slice window by clicking on Exit .
  2. select Crystal Propagation from the HRTEM card.
  3. type in the slice sequence in the reverse order: 10-1 .
  4. enter 2 for the maximum wave (the range of beams a* and b* becomes -55 and 55 ).
  5. enter a save frequency of 10 : we want to see the final result and no intermediate images.
  6. click on Start Propagation : hrm001.dif file is created.

XV-e HRTEM Image.

  1. close the Crystal Propagation window by clicking on Exit .
  2. select Microscope Propagation from the HRTEM card and close the Crystal Propagation window.
  3. hrm001.dif is selected inside the file browser.
  4. click on Propagate : after some thinking, a TEM picture will be displayed in the auto-created graph window.

XV-f Displaying and Printing a Diffraction Pattern

  1. select Display from the HRTEM card.
  2. double click on hrm001.dif inside the file browser: the diffraction pattern is displayed inside the graph window.
  3. select File from the Graphs card and Save (grf format).
  4. as is it is the diffraction pattern looks good but you still can improve it:
  5. select Hard Copy from the Controls card.
  6. click on Save : the image is saved under the name out.ps if you do not specify another name.
  7. click on Print .

This is the end of the tutorial and the beginning of your serious adventure!


XVI- SURVIVAL KIT FOR UNIX.


It is assumed here that you have an account with a username and a valid password and that you can handle a keyboard and a mouse.

XVI-a General Stuff.

NB 1 : you need to move the cursor inside a shell to make the shell active before issuing a command.

a) Creating shells

  1. go to the Desk 1 box located at the left top corner.
  2. select Tools and Shell .
  3. a shell appears wherever you click on the screen ( Fig. 22 ).

b) Moving, Sizing shells

  1. move a shell by either:
  2. size a shell by either:
  3. raise a shell by either:
  4. lower a shell by either:

Warning : UNIX commands are case sensitive !

XVI-b Directories.

The UNIX directory system looks like something in Fig. 23 :

NB : you can get info on any command by typing man commandname.

a) Listing Directories and Files: ls

ls : list all files by name
ls -c : list all files on several columns
ls -l : list all files with all info
ls -al : list all files (hidden files included)
ls .. : list parent's directory of working directory
ls ../.. : list parent's parent directory of working directory

b) Creating Directories: mkdir

mkdir dir1 : create directory dir1
mkdir dir1 /dir2: create subdirectory dir2 in directory dir1

c) Deleting Directories: rmdir

rmdir dir1: remove directory dir1
rmdir dir1/dir2: remove subdirectory dir2 in directory dir1

d) Finding the Location of a Directories: pwd

pwd : print pathname of the working directory

e) Changing Directories: cd

cd dir1: change directory
cd pathname / dir1: change directory

XVI-c Files.

a) Wildcards: * ? [ ]

ls e *: list all files beginning with e
ls e ?: list all files beginning with e followed by only one character
ls [ aeiou ] file: list all files beginning with a vowel followed by file
ls [ aeiou ]*: list all files beginning with a vowel
ls [ a-m ]*: list all files starting from a to m

b) Copying Files: cp

cp sourcefile destinationfile: copy sourcefile to destinationfile
cp /home/dir1/dir2/ sourcefile : copy sourcefile to current directory
cp sourcefile /home/dir1/ dir2/destinationfile: copy sourcefile to /home/dir1/ dir2/ and name it destinationfile
cp *.txt dir2: copy all files ending with .txt to dir2
cp filename1 filename2 dir2: copy filename1 and filename2 to dir2

c) Renaming Files: mv

mv sourcefile destinationfile: rename sourcefile, destinationfile

d) Deleting Files: rm

rm filename: remove filename
rm dir1/old*: remove all files starting with old from dir1
/rm -r filename: remove filename without asking you for a confirmation

e) Reading Files: cat

cat filename1 filename2 : (ctrl-s: stops scrolling, ctrl-q: resumes scrolling)
pg filename: same as cat but display one screen at a time the content of filename (hit return to display next page; type q to get out)

XVI-d Printing.

a) EMU Printers

mpage -2Alpsl filename: print filename pages/page on office's printer
mpage -2Alpsb filename: print filename pages/page on the basement's printer

b) VisLab Printer

lp filename: print filename on the Apple laserwriter

XVI-e Ftp, Telnet.

Telnet allows you to connect you to another computer while ftp allows you to grab or copy files that sit on another computer.

a) telnet

telnet computer.address: connects you to computer; enter your username and password when prompted
quit: ends the connection

b) ftp

ftp computer.address: connects you to computer; enter your username and password when prompted
bin: binary
as: ASCII
get filename: grab a file from the computer you made the connection to
put filename: put a file into the computer you made the connection to
bye: ends the connection

These commands are a strict minimum to know in order to use CERIUS. If you want to know more about UNIX, there is a manual somewhere in VisLab which gives a basic introduction to UNIX (you might have to do some research!).

Finally, if you have any problems (computer-related only!), shout HELP!!! and rescue should be under way within minutes in the person of Ben, Kim, Maffews or Geoff (don't ask Bernard!).


MAY THE (ATOMIC) FORCE BE WITH YOU!


Acknowledgments.


These guidelines are inspired from Vicki Keast's notes and complemented by T.C. Chou and Nicole Bordes.



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