Basics and Bonding

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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 Queen's University's Dell cluster. This is a powerful parallel computer. (Although the runs in this first exercise should take only seconds on a desktop, CASTEP is not installed in the School virtual machine.)

Please read and familiarise yourself with the Dell Login and Run instructions.

  1. First unpack the file for this exercise

    tar xvfz /home/ccpss1/CCP5SS/Exercise_1_Basics_and_Bonding.tar.gz
    cd Exercise_1_Basics_and_Bonding

  2. Study and understand the two input files provided for silicon, Si2.cell and Si2.param.
    3. You will also need Si_00.usp, a file containing the pseudopotential, but you need not try to read this.

  3. It is useful to visualise the structure first. As the visualisation tools are only on the School VM you will need to use scp to copy the files back from the Dell to the VM. Then use the cell2xsf program to create a .XSF format input file for the "XCrysden" visualisation program.

    cell2xsf Si2.cell > Si2.xsf

    Read this in and examine the structure.

    xcrysden --xsf Si2.xsf

    Familiarise your self with xcrysden's menus and options. In particular work out (a) how to turn on display of the unit cell edges and (b) how to change the covalent radius of silicon so that the appropriate "bonds" are displayed. (XCrysden knows nothing about electronic structure and bonds are drawn using an interatomic distance criterion.)

    There is also a pre-prepared file Si8.xsf which you can use to help understand the relationship between primitive and conventional unit cells of the fcc structure. (Display menu or F3/F4 keys)

  4. Now run castep on the Dell using the 2-atom cell input files.

    castepsub -n 1 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?

  5. The next task is to visualise the electron (-charge) density computed by CASTEP and stored in the Si2.check file. We use the utility castep2cube to extract the density from the .check file and convert to a .xsf file. There are 3 steps:

    1. Make a copy of the original .cell file
      cp Si2.cell Si2_cube.cell
    2. Create a new, matching .param file Si2_cube.param containing just the line
      continuation Si2.check
    3. Run
      castep2cube Si2_cube

    This will generate a number of output files in various formats. The ones you need are Si2_cube.chargeden_xsf_crystal which contains the valence electron density and Si2_cube.chdiff_xsf_crystal which contains the difference between the valence electron densities of the crystal and its constituent atoms.

  6. Copy the resulting files back to the SchoolVM

    Read the charge density into XCrysden

    xcrysden --xsf Si2_cube.chargeden_xsf_crystal

    Use "Modify->ball factor" to reduce atom sizes to make the electron density isosurface visible. Use "Tools->Data grid" to bring up the charge density visualisation panel.

    Explore using isosurfaces and plotting planes to visualise and help you understand the shape of the electron density.

    1. Can you explain what you see at an isosurface value of 0.5?
    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? Can you explain this as a consequence of the particular kind of electronic structure calculation you have just performed?

  7. Instead of the full electron density, read in the density difference file Si2_cube.chdiff_xsf_crystal. Can this help understand the bonding better than the full density?

  8. Repeat the above exercises for sodium chloride instead of silicon. Run the castep calculation using the NaCl.cell file provided (and NaCl.param,Na_00.usp,Cl_00.usp). Can you understand (from the NaCl.castep output file) why this calculation takes much longer to run than silicon?

  9. At the end of the NaCl.castep you will find a block describing a "population analysis", ie which electrons belong to which atoms. Compare this with your silicon calculation. What can you learn about the bonding from this?

  10. Prepare and visualise the electron density just as for silicon.

    Note what similarities and differences you find compared to silicon? Does this help explain the difference in bond chemistry between silicon and sodium chloride?

    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?

  11. Repeat for a metal, Aluminium using Al.cell(Al.param,Al_00.usp). Ask and try to answer the same questions as for NaCl.

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