3D Structures

This page provides several structures in the form of xyz files. The xyz format is a standard for the computer visualization of 3D arrangements of atoms. Several computer programs ("viewers") allow us to display this kind of files, and to generate images and movies from them. For example, the java-based jmol viewer is especially easy to install and user-friendly, running in most current operating systems.

You can click-download individual .xyz files and then open them with e.g. jmol. Alternatively, you may prefer to instruct your browser/OS to open .xyz files through your favorite .xyz viewer by default.

Molecules

1. C10H8.xyz
2. C2H2.xyz
3. C2H4.xyz
4. C2H6.xyz
5. C3H8O.xyz
6. C60.xyz
7. C6H6.xyz
8. CH3CH2CH2OH.xyz
9. CH3CH2OCH3.xyz
10. CH3CH2OH.xyz
11. CH3CHOHCH3.xyz
12. CH3CN.xyz
13. CH4.xyz
14. CO2.xyz
15. H2O.xyz
16. O2_hcp.xyz

Crystals or crystal-related structures

1. bcccell.xyz
2. bcccell+.xyz
3. bcccrystal.xyz
4. cannonballs.xyz
5. CsCl_basis.xyz
6. CsCl+NH3.xyz
7. CsCl.xyz
8. diamond1cell.xyz
9. diamondcell.xyz
10. diamondcrystal.xyz
11. dislocation_1layer.xyz
12. dislocation.xyz
13. fcc_big.xyz
14. fcccell_stretched.xyz
15. fcccell_WS.xyz
16. fcccell.xyz
17. fccClosePacking.xyz
18. fcccrystal.xyz
19. fcc_down_111.xyz
20. fcc_grain_boundary.xyz
21. fcc_slice_100.xyz
22. fcc_stacking_fault.xyz
23. graphene.xyz
24. graphene1cell.xyz
25. graphite.xyz
26. graphite1cell.xyz
27. hcpcell_stretched.xyz
28. hcpcell.xyz
29. hcpClosePacking.xyz
30. hcpcrystal.xyz
31. NaCl_basis.xyz
32. NaCl.xyz
33. scccell.xyz
34. sccrystal.xyz

Final notes

See here an example of a possible visualization snapshot of the graphene.xyz structure.

Several more molecular structures are available at this github site.

Notes:

• These .xyz files are are provided "as they are", with no guarantee of any specific usefulness. They are freely available for anybody's use and abuse with no copyright restriction. These files have been generated by Nick Manini, using mainly his xyz manipulation scripts, mostly available at this scripts page.
• Several periodic structures, e.g. bcccrystal.xyz, adopt oxygen as the visualized atom. This arbitrary choice comes from no specific reason: as these xyz files are just meant to illustrate some 3D geometry, any atom would do. If you happen to hate oxygen, fine: first free yourself of your nasty oxygen-breathing habit, and then replace all "O" characters in the xyz files with the chemical symbol of your pet atom, say Na. Under unix (e.g. linux or macOS) you can obtain this substitution by sed 's/O/Na/' originalfile.xyz > substitutedfile.xyz
• Several structures named XXXcell.xyz or similar do not represent one single primitive cell, but usually several cells, or one cell plus a few more atoms, usually useful to visualize geometric symmetries.
• Several of these structures illustrate the textbook Introduction to the Physics of Matter by N. Manini.