Rep:Mod:phys3 intro
Making a Wiki page
Formatting
Example of Bad Formatting
The below JMol object is too small to read, and the .gif below that is too large. In addition, the orientation of the JMol prevents the reader from seeing what's going on. You should aim to keep your page relatively compact while allowing the reader to see all the necessary data.
Example of Good Formatting
Here, the JMol and .gif are grouped together in a table. The context is provided below so the reader doesn't have to guess.
| Anthracene/Maleic Anhydride TS | |||
|---|---|---|---|
| JMol | IRC | ||
|
| |||
| Figure 1: An animation (left) of the imaginary frequency (-467cm-1) and the IRC path (right) of the reaction of Antracene with Maleic Anhydride. Optimisations were performed with B3LYP/6-31G(d) | |||
Use tables to organise your data, and support your data with text. Just as with reports, reference your figures and tables.
General Reminders
Uploading Images
You must not give your images "obvious" names. This is because every image is stored in the same location, and a duplicate name will cause an overwrite. This is obviously bad for the person whose data you overwrote, but could also mean your data will be overwritten! It's a good idea to add your username to the image name when you upload.
Bad name: Diels_Alder.png
Good name: fwj10Diels_Alder.png
Save images as png files and animations as gif files. .tif files (the default for GaussView) are not recognised by wiki.
Multiple Pages
If you find your page is too cluttered - such as with summary tables and proof of convergence for multiple optimisations - you can create a second page to act as a supporting information page. This can help you to organise your work. Remember to provide links and make it clear that you have done this!
JMol Objects
Although useful, JMol can use up a lot memory if there are too many on the page. It is possible to have "popout" Jmols that open in a new window, or a link to another page. >10 JMol objects would probably be too many.
Editing and Saving the Wiki
Wiki allows two methods of editing: in-place editing ("Edit") and source code editing ("Edit source"). There are advantages and disadvantages to each of these.
In-place Editing
Clicking "Edit" will allow you to edit the page while preserving the format. It comes with a few tools to help you edit and is easier to learn. However, it gives little control over certain aspects of formatting.
There is a bug that prevents saving from this editing mode. Essentially, it gets stuck on "Saving page..." and fails to save. To prevent this, click on "Edit source" instead of "Save" and keep changes. Save the page from here.
Source Editing
The alternative is "Edit source". The source code of the wiki page will be displayed without formatting. This method is harder to get used to, but allows a huge amount of control, including applying script to JMol files (for example, vibrations and orientations).
Have a look at the cheatsheet to see some of the available options. You can also view the source of other pages to see how a certain format was achieved, but beware of plagiarism.