Beyond Webmo

Once you have gone through the Undergraduate Worksheet you should understand how to run basic molecular modeling calculations. The next step is to learn to use more advanced codes that let you model solids and surfaces, such as VASP and CP2K. Follow these steps to help you learn these codes. Don't hesitate to ask for help from group members on any of these. They are here to help. Talk to other people!

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1. Get an account on our linux systems, Turing and/or Ace.
2. Login to our linux systems. With windows you can use Putty. With mac or linux you can "slogin turing.wpi.edu" at the command line to login.
3. Learn how to upload files to our linux systems. Filezilla is one software you can use. There are others also.
4. Learn Linux/Unix after you've logged into our linux systems. You'll need to know how to use the command line to change directories, copy files, run commands, etc.
5. Get some basic input files for CP2K or VASP. Ask Prof. Deskins which program you should learn. Ask for basic input files from someone in the group. These should be simple molecules, like water, methane, etc. Put them in a directory for the job(s) you'll run. Here's some resources to Learn CP2K, including input files. The VASP wiki is a great place with tutorials and other information. The CP2K website also has lots of good resources.
6. Submit jobs using the basic input files. Ask for help on submitting a job. We have a queue system to control what jobs are running on the computers.
7. Monitor your jobs in the queue. Learn how to check that your jobs are running or if they've finished.
8. Look at your output files (OUTCAR for VASP and something.out for CP2K). Learn how to check the energy, the forces on the atoms, and whether a job converged.
9. Download the output geometry files and view them on your computer. Programs you can use to view geometries include VESTA, ASE, Jmol, or Avogadro.
10. Develop a system to keep track of computer jobs and results. You'll need to keep track of what jobs you've run, their energies, and possibly other information. You'll also need to calculate stuff (like reaction energies) from simulation outputs. A spreadsheet is a great tool for this.
11. Learn what input files are required for your job to run, and what they do. Check the VASP or CP2K manuals/tutorials for help.
12. Learn what output files are produced by the code. Learn what information is in the various output files.
13. Learn how geometry optimization works and why it's necessary. It's helpful to understand what a potential energy surface is and why the energy minimum is important. The chapter "The Concept of the Potential Energy Surface" from Computational Chemistry by Lewars (available as an e-book from the WPI library) may be useful. Here's another useful resource. Geometry optimization is ultimately an energy minimization problem, so it may be useful to understand a little about numerical minimization and the algorithms involved (e.g. conjugate gradient) since you may need to change algorithms or algorithm parameters to optimize some geometries.
14. Learn how wavefunction convergence works. A good computational chemistry or molecular modeling book can provide details on this.
15. Explore changing parameters in the input files for simple molecules and run new jobs. Learn what effect changing these parameters have (look at output and geometries).
16. Make your own molecules for simulation. You can use Avogadro or ASE to "draw" new molecules. Take the xyz coordinates from the software and create input files for these molecules. Run these new jobs. Make sure the outputs are all ok.
17. If you haven't read the first four chapters of "Density Functional Theory: A Practical Introduction" by David Sholl and Janice A Steckel (available from WPI library), do so now. Or review them if you have read them.
18. Learn about periodic structures of solid materials, like unit cells. Wikipedia has an article on crystal structures. A basic materials science book should also have details on crystal structure.
19. Model a bulk material, like TiO₂ or Pt. Ask Prof. Deskins which material you should model.
20. Calculate the most stable lattice parameters for your material. This page on Calculating Lattice Parameters should be helpful. Compare your results to experiment or other density functional theory results.
21. If you don't understand about slab models, learn more about them. Chapter 4 of the Sholl book may be helpful.
22. Model a bare surface for your material. Get files from members of the group or Prof. Deskins. Look at the output (energies, forces, geometry) to verify that everything is ok.
23. Model adsorption of simple benchmark molecules over your surface. Calculate adsorption energies and compare with our own previous adsorption energies, or adsorption energies in the literature.
24. Talk to Prof. Deskins about the next steps in your research, or what systems you should model.
25. Before you start production quality calculations send Prof. Deskins your input files to ensure everything is in order.