Visualize the Structure

It's always nice to be able to visualize a structure and save a picture so that we can later reminisce about how good we were with using PAW. The program comes with a tool which will help us do just that.

• Use paw_strc h2co, which will create an h2co.cssr file for the molecule in cartesian coordinates (angstrom) that you can use to visualize the structure in Cerius². Also, back up this file because we are going to write out a different version of it:

  
  

  alpha:~/tutorial/h2co> paw_strc h2co

  MOLECULAR OUTPUT PRODUCED

  ======= TASK FINISHED ========

  alpha:~/tutorial/h2co> ls *.cssr

  h2co.cssr

  alpha:~/tutorial/h2co> mv h2co.cssr h2co-m.cssr

  
  

• Use paw_strc -c h2co, which will create an h2co.cssr file for the latice that you can use to visualize the structure in Cerius²:

  
  

  alpha:~/tutorial/h2co> paw_strc h2co

  CRYSTAL OUTPUT PRODUCED

  ======= TASK FINISHED ========

  alpha:~/tutorial/h2co> ls *.cssr

  h2co.cssr h2co-m.cssr

  
  

• So the h2co.cssr file has the crystal structure, and the h2co-m.cssr file has the molecular structure. One can then use the former to visualize the spacing and determine if your lattice constant is sufficient for the system you want to examine. If it's not, you will see the resulting problems with the ctructure visually. Give it a try, and print an image showing bond lengths.
• Next, we will do some data analysis . . .