Overview

Carrying out calculations

• Some of calculations can be carried out on your laptop but others are too large for the laptop and must be carried out on the the servers within the High Performance Computing or HPC facility via the online portal.
• It will be clearly stated in the instructions where a calculation should be carried out.
• Instructions can be found here submitting calculations to the departmental SCAN cluster (you will be given this link again later when you need it)
• Calculations are normally carried out in a UNIX or LINUX environment and these are sensitive to special characters (anything that is not a letter or a number) and spaces, so to get into good habits from the begining you should never use special characters or spaces in your file names. Repeat: do not use spaces in file names.

Week 1: Learning How (30%)

• Day 1 carrying out basic calculations, learning new things, examples with detailed instructions:
  • start by creating your wiki page
  • creating a molecule
  • optimising a molecule
  • analysing the output
  • understanding optimisations: part a
  • understanding optimisations: part b
  • update your wiki page
• Day 2 carrying slightly more complex calculations:
  • basis sets and pseudo-potentials
  • using a better basis set
  • using pseudo-potentials
  • using Scan servers
  • publishing in DSpace
  • mixing basis-sets and PPs
  • structure comparison
• Day 3 calculations that provide information:
  • vibrational analysis theory
  • carrying out a vibrational analysis
  • animating molecular vibrations
  • vibrational comparison
  • molecular orbitals
  • NBO analysis
• Day 4 calculations that provide information, rapid feedback and project choice:
  • reaction energies
  • comments on accuracy, energies and symmetry important
  • complete your wiki for part 1 of the lab
  • important all students should come to the lab for rapid feedback between 2-4 and show your wiki to a demonstrator for feedback
  • after your rapid feedback you must see the senior demonstrator to select your mini-project, this can be from those provided below or one of your own! However, the projects are allocated so as to distribute them evenly, thus if you are late you may not have a choice.
  • There is a 0.5 mark bonus if you select your own project. To be eligible to choose a project you MUST have almost completed your first weeks wiki on Friday (week 1). Your project ideas must be discussed with Dr. Hunt or Dr. Matthews 2-3 pm Friday, and they must be authorised. Here are some guidelines for selecting a project. These requirements are for your own benefit, they will save you from starting something too complex for you, or too large for the time available.

Week 2: Mini Project (70%)

Now it is time to put all you have learned to work, and to start your Mini Project.

• Some key instructions! Important READ THESE
• carry out your calculations on the HPC servers, for every calculation undertaken provide a link to the file on "D-space"
• if a job has not converged in 50 steps you MUST get a deomonstrator or lecturer to look at it.
• time management is key, NO calculations should be carried out on the last day, leave this time for completing your wiki.
• for each structure optimised provide the "summary", the "Item" table, the "low frequencies" lines and show that there are no negative frequencies.
• use your data! at least 50% of the project should be centered around interpretation, compare and analyse your data, can you find a justification or interpreation for trends? Are you able to rationalize, using this information, some key property or chemistry of the compound?
• simply reporting your results will only gain you a maximum of 50% of the mark for the project
• follow as similar pattern of steps from week one, the instructions for the mini projects are less developed, because you are now expected to know the processes (from week 1) and you are expected to work with more independence.
• here is an example of very good project wiki page from a previous student (Celeste van den Bosch, used with her permission) to give you an idea of what to aim for example project.
• Project options:
  • Lewis acids and bases
  • Investigating aromaticity
  • Ionic liquids, designer solvents
  • option 4

Removed

Advanced for those who are interested (this is voluntary!): following a reaction path, the quantum nature of ammonia

• about ammonia
• symmetry and its impact
• the effect of using different methods
• following the inversion path
• the vibrational connection