Structure formats

General comments

Some important things to note about structure formats used in CDE:

• Throughout CDE, we use simple xyz files as input/output formats.

• You can use openbabel to convert from a wide range of files to/from xyz files.

• A convenient program for creating initial structures in xyz format is Avogadro.

• The coordinates in an xyz format file are in units of Angstroms.

• If performing NEB calculations, the number of snapshots (or configurations) in the xyz file for the full path should be the same as that defined in nimage in the input file.

xyz format

• Each xyz frame or file looks like this:

  3
  Simple structure demonstration  
  C 0.000  0.000 0.0000
  O 1.50   1.670 5.6708
  H 2.0   3.54.  3.14
  

• The first line contains the number of atoms, the second line is either a blank line or a comment line.

• After the comment line, the file contains a list of atoms with their atomic labels and (x,y,z) coordinates in Angstroms.

• Different frames in an xyz file follow each other immediately, like this:

  2
  
  C 0.000  0.000 0.0000
  O 1.50   1.670 5.6708
  2
  
  C 0.1500  0.2166 0.007
  O 1.56  1.679  5.7098