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1 Bonding

Learning Objectives

  • Introduction to CASTEP input and output files.
  • Running CASTEP on the STFC Workspace.

Introduction

The aim of this exercise is to familiarise you with CASTEP input and output files and running the code, some associated utilities and conversion programs. You will run some simple and small CASTEP calculations on canonical examples of covalently and ionically bonded materials - silicon and sodium chloride - and use the results to study the bonding from an electronic structure perspective.

While performing the exercises try to think about the reasons for each step, and about how to interpret the results. The point of the exercise is not merely to reach the end but to learn the path. The exercise below contains a number of questions. Please take note when a question is asked of you, and think about the answer. Feel free to discuss the answer with one of the demonstrators after you have thought about it for a while.

The secondary aim of this exercise is to learn to run programs on the STFC Workspace. This is a powerful cloud-based machine and each participant has access to an individual CPU with 16 cores. (Although the runs in this first exercise should take only seconds on a desktop.)

Where To Find Help

If you want more information about a particular CASTEP keyword, or you want to find if CASTEP has particular functionality, there are a few places you can look.

  • There is information on this website: www.castep.org.

  • CASTEP has an in built help option to assist with using particular keywords. Information on using CASTEP can be seen by using:

    $ castep.serial --help

    To get more information on a particular input file keyword (e.g. kpoint_mp_grid) use:

    $ castep.serial --help kpoints_mp_grid

    If you don't know the keyword you need to use, then you can search on a particular keyword. This returns a list of keywords that you might be interested in, e.g. to look at all keywords which contain a reference to symmetry.

    $ castep.serial --search symmetry

    Finally, to list all keywords, use:

    $ castep.serial --search all

    Note that the long-form arguments --help and --search can optionally be replaced with -h and -s, respectively.

Example 1 - Silicon

  1. Copy the files to your user directory

    $ cp /course_materials/Si2.tar.gz .

  2. Unzip and untar them, then move into the new directory

    $ gunzip Si2.tgz
$ tar -xvf Si2.tar
$ cd Si2

  3. Examine the CASTEP input files Si2.cell and Si2.param using your favourite text editor (e.g. nano). The Si_00.usp file is a pseudopotential file, you do not need to understand it at the moment.

    $ nano Si2.cell
$ nano Si2.param

  4. It is useful to view the structure before submitting your calculation using CASTEP. You Jmol and Vesta are installed on the VM and can both be used to visualise the Si2.cell file.

  5. Cell Structure Visualisation

    • Jmol

      To open the Si2.cell file using Jmol: Open Jmol from the applications menu. then use File => Open and navigate to your Si2.cell file. Alternatively, you can drag and drop the Si2.cell file into the Jmol window, and Jmol will open it. It can be helpful to view multiple repeat units of your unit cell. The easiest way to do this in Jmol is to open a console window, click File => Console and type:

      $ load "" { 2 2 2 }

      to show a 2x2x2 supercell. Check the geometry of the input file is what you expect it to be before moving onto the next step.

    • Vesta

      To open the Si2.cell file using VESTA: Open VESTA then use File => Open and navigate to your Si2.cell file. You cannot drag and drop into VESTA.

    If you wish to create a supercell as above, use Objects => Boundary. Then edit the maximum and/or minimum values of x, y, and z in order to change your boundaries. Setting x(max), y(max), and z(max) to 2 will create the 2 by 2 by 2 supercell as above.

    Check the geometry of the input file is as expected before moving on to the next step.

  6. Now run CASTEP using the 2-atom input files.

    $ castep.serial Si2

    This should only take a few seconds and produce a readable output file Si2.castep. Examine this file and try to understand the meaning of the various parts. In particular check the section following the header which lists all of the input parameters, both explicit and default. Note what default values of the major parameters CASTEP chose where you did not specify them explicitly. (There will be some whose meaning has not been explained. Don't worry about these.)

    • Find the section of the file which monitors the SCF loop and the approach to convergence. How many SCF iterations did it need?

  7. Visualisation of the charge density

    • Jmol

      Jmol can also be used to view the isodensity map, open the .castep file by dragging and dropping the Si2.castep file into the Jmol window.

      Open the Jmol console (File => Console) and type the following commands:

      $ load "" { 2 2 2 }
$ isosurface rho cutoff 14 "Si2.den_fmt" lattice { 2 2 2 }

    Note: you can use the cd command within Jmol to navigate to the folder with your .castep files.

    Jmol uses forward slash for paths to files on windows and linux based machines. This Si2.den_fmt file is a formatted file produced by CASTEP that contains the value of the electron density on a grid of points. This isosurface command in Jmol plots an isodensity surface over your atomic positions.

    • Vesta

      You will see a file called Si2.den_fmt which contains the charge density in a formatted (i.e. a human readable, ASCII file). We need to change this file into a format Vesta can read. Copy it to a file called Si2.charg_frm
      cp Si2.den_fmt Si2.charg_frm

    Now edit the file Si2.charg_frm with a text editor to remove the first 11 lines. The file should now begin with 1 1 1 and a number. You can now open Si2.charg_frm with Vesta. Note that Vesta needs both the .cell and .charge_frm files to make a plot. If you are working on a remote machine you will need to copy both of these back to your local machine to view with Vesta. You can find a walkthrough video of this process here.

    Silicon Charge Density

    An alternative way to plot charge densities (and much more besides) is c2x. You can use c2x to convert the .den_fmt file to a .xsf file which can be read by Vesta:

    ```
$ c2x -c Si2.den_fmt Si2.xsf
```

    Answer the following questions:

    1. Can you explain what you see as you vary the isosurface value?
    2. Can you see any features which might be characteristic of a covalently-bonded crystal.
    3. Do you notice anything strange about the electron density close to the Si nucleus?
    4. Can you explain this as a consequence of the particular kind of electronic structure calculation you have just performed?

  8. Repeat steps 1-8 using input files for sodium chloride and aluminium.

    /course_materials/Al.tgz
/course_materials/NaCl.tgz

    Think about the following questions:

    • Note what similarities and differences you find compared to silicon?
    • Does this help explain the difference in bond chemistry between silicon, sodium chloride and aluminium?
    • Does this help explain why there are many reasonable classical potential functions for NaCl to be found in the simulation literature, but that finding good potentials for silicon is a very tough challenge?
    • What about aluminium, can you find good potentials for aluminium?