View source for Mod:laptop

See also: [[Mod:org-startup|1C comp-lab startup]], [[Mod:timetable-1C|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1C Script]], [[Mod:toolbox|Module 1C Toolbox]], [[Mod:writeup|Writing up]], [[Mod:dont_panic|Don't panic]], [[Mod:inorganic|Inorganic Computational lab]], [[Mod:phys3|Physical computational lab]].

= Using a Windows  laptop for the course =

This section describes how to use your course laptop running the  Microsoft Windows 7 operating system,   and what to do if you need technical assistance with it.

'''We trust you to treat the laptops supplied for this course with care. If a laptop is returned with damage beyond "reasonable wear", you will be liable for a flat fee of £50.  Seriously damaged or lost laptops will be evaluated on a case by case basis: you will be liable for the cost of purchasing a replacement laptop, although if documentation is provided, extenuating circumstances will be taken into account.  Please note that it is a requirement for graduation that any lost or damaged laptop is paid for (similarly for library debts).'''

The laptop contains in one simple and portable package all the software you will need to complete this lab; however students are not obliged to accept the laptop under the conditions we  have set, you can use the desktop computers provided in the study and computer room areas (although these are on a first come-first served basis).  Potential lab grades will not be decreased in any significant way by not taking a laptop.

== Course Laptop Pickup and configuration ==

#The first day of the course will include acquiring the course  laptop, and familiarizing yourself with its use. It should be collected on Monday from '''DeeJay in room 237, from 12:00 - 13:00''' on the first day of a 2-week lab session. It should be returned two weeks later  on '''Friday  to DeeJay in room 237, from 12:00 - 13:00'''.
# Before you start it up, ensure the Wireless is on (3rd LED from right above the keyboard; if it's not on, press the LED button to switch it on). You should also be in a Wireless zone as well (most of the chemistry department is such). 
#Windows 7 Enterprise loads at startup. After the boot is complete, log yourself in ( the  domain ''IC'' is pre-selected).  This should progress as per any desktop login and will result in all your credentials  being '''cached''' on the laptop. You might get an initial error message,  but a second attempt at login normally fixes this problem. 
#* You will also require this cached profile if you want to use your laptop online at home, or outside the department/college. '''So log in (and out again) before you take the unit home!'''
#The Laptop comes without an ethernet  '''patch cable''' for use with wired network, which you might need for home use if you do not have a wireless router there. You can get such ethernet cables for a small amount in most computer shops.  You might also want to plug a  USB or Bluetooth mouse in as an alternative to the trackpad.
## If you put the laptop into hibernate mode (by closing the lid and leaving it closed for  ~10 seconds), it may take a little while to re-establish the connection when you re-open the laptop.
#If you use '''Firefox''' as your browser  and try to connect to the chemistry wiki, you may get a '''Secure Connection Failed''' page appear, just click on the "Or you can add an exception..." link and click the "Add Exception" button,  then "Confirm Security Exception".  You should then be given access to the chemistry wiki site.

== Laptop use and file storage whilst at Imperial ==

#Your laptop should run for about  6 hours from a full charge.  If you do need to charge it during a working day, please do so in the study or the tutorial rooms on level 2. 
#If you are working  in College, and have the laptop online (via either a wired patch lead or the  WiFi), then store everything in the usual place ('''H:''').  Alternatively, you will find a drive labelled '''D:''', which is in fact part of the hard drive on the system.  You should use this if you are offline. This drive has a total capacity of  around  50 Gbytes (compared to 500 Mbyte for drive '''H:''') so you can also use it to store very large files. Be aware however that whilst drive  '''H:''' is backed up each night,  drive '''D:''' will not be backed up at all (so if the laptop fails, or is stolen, you will lose everything).  We suggest you store your key results on both drives!

== How fast are the laptops? ==

Computational chemistry modelling varies wildly in the amount of computer time need. Thus most molecular mechanics and semi-empirical MO calculations take just seconds, or a minute or so. These are all done on your laptop. The ''ab initio'' and ''DFT'' procedures can be much more time consuming, and now the issue arises of whether they should even be attempted on your laptop. 
# The laptop is a lightweight model with a battery charge that lasts for a reasonable working day.  The processors are fast enough for you to attempt Gaussian calculations on small molecules (typically the size of eg decalin). If you do attempt such a calculation, you will immediately notice that the fans on the laptop may kick in very soon, and the unit may get quite hot! For this reason, you should never attempt to run such a calculation for much more than about 1 hour. Under no circumstances should you attempt to leave it running ''e.g.'' overnight! 
# If it turns out you do need to run for  > 15 minutes, then submit to the batch subsystem ([https://scanweb.cc.imperial.ac.uk/uportal2/ SCAN])  we have set up for you to use.  Not only are the computers you will use there at least 20 times faster than the laptops, such jobs also do not compromise your ability to continue using the laptop; they also let you run multiple jobs concurrently. Last but not least, the SCAN will allow you to deposit the job in the digital repository as a clear and permanent record of your calculation.

== Technical  Help ==

#If you are having problems with the laptop, take it to the  ICT support desks, in either Sherfield level  4, or Room 135 in chemistry  C1. '''IMPORTANT'''  A small number of systems might show abnormal instability.  This manifests with unexpected and total freezes 3-4 times a day or more. If you experience this, do not simply wait for the problem to resolve itself, but arrange to have it swapped for a hot spare. Sometimes hardware faults (or e.g. memory modules that might have become unseated, or simply faulty) will cause this, and the system will probably benefit from a thorough checkout.  As  a very approx rule of thumb, if the Laptop does not display the chemistry background seen on other departmental computers, it is probably going to misbehave.
#You may also wish to keep an eye out on the  [[Mod:latebreak|late breaking news]] page for general updates, and the discussion areas for [[Talk:Mod:organic|Module 1]], [[Talk:Mod:inorganic|module 2]] and [[Talk:Mod:physical|module 3]] where people document their experiences, suggest bug fixes etc.

== Activating Java ==

Test using [http://www.java.com/testjava/ this link] whether Java is activated for your browser. You may need this for your Wiki.
# You may get an '''inactive plug-in''' message from the above site. Click on that text to activate Java.  If you get messages about the  Java being out of date, ignore them and continue.

== Laptop use at  home ==

The advantage of having  your personalized  laboratory  is that you can complete experiments wherever you wish, and not just in the  Imperial College precincts. Proceed as follows:

# You will have to go online at  home.  Since this varies according to the ISP service you have, you will have to arrange this yourself  (via your ISP if necessary). If you are using WiFi at home, configure it as per above.
# [[image:vpnicon.png|right]]In order to edit the  Wiki for your project, you will need to establish a [http://www3.imperial.ac.uk/ict/services/securitynetworkdatacentreandtelephonyservices/collegenetwork/networkconnections/vpnconnection VPN connection] as part of this process.  An icon on the desktop is available for this purpose.
## To mount your drive  H:, find out its network address: [https://www.imperial.ac.uk/spectrum/ict/dynamic/homedir/homedir_location.asp Home Directory Location] and [http://www3.imperial.ac.uk/ict/services/networks/networkconnections/vpnconnection/homedirectory follow the instructions].
#You can also use your own laptop (as opposed to the loan laptop), but please be aware that much of the software installed on the  course laptop described in the previous section may be missing since the site licenses we have for it will not apply to your personal laptop.  There is '''one exception''' to this; the site license for '''ChemBio3D''' does allow any student with a valid Imperial College email account to install it on their own laptop. To invoke this license, connect to [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 this site] and  follow the instructions. This license will last until 2014.

=Using a MacBook Laptop for the Course =
== First  Login ==

[[File:login-wifi.jpg|right|200px]][[File:login-cable.jpg|right|100px]]To enable use off-campus, the first time you use the laptop you have to log into your  College account, using a network cable and Ethernet-Thunderbolt adaptor '''in College'''.  Such an adaptor will be available to borrow for this operation (which will take  2-3 minutes). Proceed as follows:
# The image with the red dot on the right illustrates what you see when a network cable is not plugged in. Once you have plugged in a cable, wait 15 seconds and it’ll go yellow then disappears. 
# Now proceed to log in using your  College login.  The first time you do this will take longer than subsequent logins.  
# The process  '''caches''' your credentials, so that you will then be able to log in even if you have no active network.

== Subsequent logins ==
[[File:Dock2.jpg|right|170px]]The next time you log in (this time without a cable),  you will need to activate the WiFi connection.  
# '''Apple menu on top lhs/system preferences/Network''' will reveal the WiFi configuration (tick the box show WiFi status in menu bar). 
# Select the network name '''Imperial-WPA''' and enter your college credentials to connect.  This setting will be remembered, and next time the laptop comes within range, it will automatically connect.
== Using your own  Mouse ==
If you do not feel comfortable using the  trackpad, do connect a  USB mouse  (or Apple Wireless bluetooth alternative).

== Activating Java ==

Test using [http://www.java.com/testjava/ this link] whether  Java is activated for your browser.  You may need this for your  Wiki. 
# You may get an '''inactive plug-in''' message from the above site.  Click on that text to activate Java.

== Populating the  OS X Dock ==
Next populate the  OS X dock with a few (chemistry) applications.  Proceed as follows:
# Go to '''Finder/Preferences''' from the top level menu, and tick the  '''Hard disks''' item on the desktop. This reveals the hard drive. 
# Double click the hard drive and then the '''applications''' folder to reveal the contents
# Drag the following icons there to the dock at the bottom:
## Avogadro (ChemBio3D is not available for  Macs, and so Avogadro is used as a replacement)
## ChemDraw 13
## FireFox
## Open the folder  '''Gv-5.09''' and drag  '''gview.app''' to the dock
## TextWrangler (use this instead of  NotePad++ on  Windows)
## Open the folder  '''Utilities''' and drag  '''terminal''' to the dock
## And any other applications you wish to your dock as well. 

You should only need to do this once.

=== Using the Dock ===

[[Image:Dock4.jpg|300px|right|thumb|Using the dock]] Once your dock is populated you can do most things from the area.  In addition, one of the icons represents your '''H: drive''' (the same one you have on your Windows login) and so you can get/put files from there.  

The other icon is the downloads area, where all downloaded files will appear, and you should navigate to that when required (Avogadro etc).
=== Mounting the H: drive ===
Mounting the  H: drive is something of a chicken-and-egg situation, which results in the  H: drive initially being unavailable. To mount it after login, '''Finder/Go/Connect to server'''.  There enter  '''smb://ic.ac.uk/homes/<username>''', click the '''+''' to add it to your list of servers and then authenticate with your password.

<!-- == Licensing ChemDraw ==
The provider of  ChemDraw has issued us with a very unfriendly licensing scheme, which requires every user to license the product for themselves on every  Mac computer they use (we have requested a more flexible license from them).  Proceed as follows (this is a one-off per computer, per user).
# Start ChemDraw.
# Log into this Wiki, and edit this paragraph to expose the licensing information.
# In the license request, enter  .......   7650416   as the serial number
# For the activation key enter .......   36VW-HL77-C7WY-XSO7-DO 

-->

== Licensing CCDC/Conquest ==
Enter the Site No. as 183 and the confirm code as 52CA2F

== Screen shots on a  Mac ==
You will need to capture images on the screen for inclusion in your report.   This is best done on a  Mac by pressing the '''cmd''',  '''shift''' (above the ctrl key)  and '''4''' from the numerals at the top. This produces a cross-hair cursor, using which you should drag out the area you wish to capture.  When you release this cursor, a screenshot is saved on your desktop, of  type '''.png'''  You can upload this file from the desktop into the Wiki.

== Running Gaussian  on the  laptop ==
This is normally invoked from the Gaussview program.  Defaults have been set up to use four processors and  2Gb of memory, which makes the laptop run flat out.  You may find other operations sluggish whilst it is running.

It is also possible to run  Gaussian from the  '''Terminal''' Window by typing <code>g09 yourinputfile.gjf</code>
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See also: [[Mod:org-startup|Synthesis comp-lab startup]],[[Mod:timetable|Timetable]],[[mod:laptop|Laptop use]], [[mod:programs|Programs]],[[mod:organic|Module 1C]],[[Mod:inorganic|Inorganic Computational lab]],[[Mod:phys3|Physical computational lab]],[[Mod:writeup|Writing up]]