Creating a wiki page

Make a blank wiki page

  • Your report is in the form of a wiki page
  • It is easiest to create your wiki page now and to populate it with information as you go, treat it like a workbook
  • Near the end of the lab you can put all the formatting in place so that the information is nicely presented, don't try to hard to make it "pretty" as you work through the lab, you may waste a great deal of time this way
  • Start by creating a page: step by step basic instructions for creating a wiki
  • Here is my first attempt:

    Yr1testPg_first

Populate your wiki page with some simple headings

  • Click on "Edit this page" and put in a few headings, for example: "NH3 molecule", and "Project molecule" (I made mine bold).
  • Here is what mine looks like:

    Yr1testPg_NH3info

  • when I saved it, it lost all the line breaks, so I clicked on the "edit" (shown in the red box) and NOT "edit source" tab and added the line breaks:

    Yr1testPg_edit

  • if you get stuck goto my page and look at the "source code" by choosing "edit source" comp_chem_lab_testpage (do not change anything!)

If you have just started go back to the main lab now

Moving on to more complex things

  • you should copy and paste the "Item" part of your output file into your wiki. Surround this section by the "<pre>" and "</pre>" tags to ensure the formating is kept, for example

    <pre> 

             Item               Value     Threshold  Converged?
 Maximum Force            0.000323     0.000450     YES
 RMS     Force            0.000153     0.000300     YES
 Maximum Displacement     0.001116     0.001800     YES
 RMS     Displacement     0.000922     0.001200     YES

    </pre>

  • You can find here how to
    • add images
    • add rotatable 3d images (Jmol) of your optimised molecule
    • link to a file in Dspace
    • link to a file run on your laptop
  • Save and preview your page constantly (this makes a new version, which you can always revert to) if you run into a problem and cannot reverse it.
  • See also Backing up your report this is important when you are adding jmol files as if you do something wrong you can hang the application!

What do we expect to see for EACH molecule on your wiki-report page?

  • We expect to see:
    • key information about the calculation, such as method (eg B3LYP) basis set (eg 6-31G(d,p) and symmetry (eg C3v)
    • the Item table copied and pasted into your wiki
    • a rotatable 3d jmol file/image of the optimised structure
    • a link to the final file of the optimisation/frequency
  • Each gaussian file is given a unique identifier and we use these to check for plagerism.
  • Failure to include a valid link and/or valid log file will result in 1 mark deducted for each missing file (a broken link = missing file). Check that all your links work!
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